In a Vacuum – 1/2 – Sunfire

Title: In A Vacuum
Author: Sunfire
Fandom: Stargate Atlantis, NCIS
Genre: Crossover, Drama, First Time, Hurt/Comfort, Romance, Slash
Relationship(s): John Sheppard/Rodney McKay, Tony DiNozzo/Ronon Dex
Content Rating: R
Warnings: Indirect Mention of Child Abuse
Author Notes: Huge thanks to my awesome artist, Mizu Sage, who made such a beautiful book cover. It’s a fabulous visual of my story and adds so much! Thanks also to my beta NCP, you’ve the patience of a saint. FYI- Timeline Shenanigans: I shifted SGA a couple of weeks to line up better with SWAK, gave Tony 6 weeks to recover post plague, and compressed the time between some events in NCIS to make it fit the story arc. I also hand-waved away the existence of Landry and left O’Neill in charge
Beta: NCP
Word Count: 62,595
Summary: Weir abandons Atlantis in order to ascend, John and Rodney clean up her mess while ignoring their feelings for each other, and Tony uses his renewed friendship with Lt. Col. Sheppard to cope with life in DC and escape NCIS. Somehow, it all leads to a better Atlantis, steamy McShep, ZPMs, and Ronon checking out the hot new Agent Afloat.
Artist: Mizu Sage



 Chapter One

The first thing John saw when he beamed down to the city from the Daedalus was an extra six Marines in the ‘Gate room and Dr. Miko Kusanagi, of all people, arguing with Bates in front of the open doors to Weir’s office. He had known that something was going on when the Sargeant had been the one to contact the Daedalus when they entered radio range on their trip back to the city. But this wasn’t what he was expecting.

“What is going on here? Where’s Dr. Weir?” demanded the military commander with only a glance at Caldwell.

As the highest-ranking military officer, it was within the older man’s rights to take command of the situation, but from the look on his face, he planned to enjoy watching Sheppard deal with whatever was going on in his city. He stayed pointedly silent as the Lt. Colonel mounted the stairs.

“Sir,” Bates said in a tone that lacked as much subtly as it did respect. The small Japanese scientist interrupted before he could continue.

“Col. Sheppard, proper readings must be taken or nothing can be known for sure. I must examine the computer to ascertain the situation in full. The office has been cleared by military personnel. My team requires access. Sgt. Bates refuses to let me do my job.”

“This is a military situation and I am in charge. You-”

John cut off whatever Bates was going to tell the normally shy young woman, forcing the head of security to finally face his commanding officer.

“Sargeant! If a situation exists that puts this city under military command, I am the one in charge. Now you will explain to me the situation and I will decide whether that’s the case.”

Dean Bates clenched his jaw for a few seconds before biting out a response. “Dr. Weir has disappeared and there is a possible threat to the safety of this city. The MPs will look through this room before any scientists are allowed inside. It’s a matter of security. I am doing my job, Sir.”

Dr. Zelenka spoke up from where Rodney had joined him at a console in the control room. “All evidence points to Dr. Weir ascending late last night, Col. Sheppard. But to be sure, we need to take scans and make exam of office to see if she did intentionally.”

“She ascended?” Sheppard said, without any inflection whatsoever. He held up a hand when both Bates and Zelenka started to respond simultaneously. “Okay. From the top people. What exactly happened?”

They both began speaking once more. John determined he really had to revise his opinion of the female scientist when it was Miko who called out decisively over the conflicting voices.

“Colonel.” Surprisingly, everyone in the room quieted, allowing her to be easily heard as she went on in a softer but still resolute tone. “If I may?”

Suppressing a smirk, John nodded at her in permission, absently noting the angry expression blooming on Bates’ face and the slightly surprised but otherwise non-pulsed look on Zelenka’s.

“Dr. Weir was last seen three days ago entering her office and engaging full privacy, though it was indicated in the logs that she exited the office two days ago for one hour and twelve minutes before re-entering and once more engaging privacy locks and settings.”

The eyebrows of everyone who had been gone on the Daedalus raised in surprise but no one interrupted.

“She cancelled all scheduled meetings electronically during the time she was locked in her office. The only outside contact with her was a radio conversation with Dr. Beckett yesterday morning when he inquired about her health, to which she responded that she was fine but had some sensitive paperwork to complete and did not want to be disturbed.”

John glanced briefly to the man in question and saw him nodding along with the woman’s account so he turned his attention back to the almost military report she was giving him.

“Last night at approximately 11:45, Lt. Banks, stationed in the control room, saw a sudden bright flash of light through the covered windows of Dr. Weir’s office. She attempted to enter the office but was unable to disengage the lock or privacy setting. Dr. Zelenka was asked to come bypass the lock.”

Bates tried to cut in but closed his mouth with a scowl when Sheppard shot a hard, warning glance at him. Miko ignored the near interruption and kept speaking.

“Dr. Zelenka attempted a standard override and was unable to gain access to the office for several hours. I was tasked with accessing the security footage for the office, control room, and surrounding hallways. That footage showed no unexpected traffic, and no one entering or leaving the office other than Dr. Weir, at the times I stated before. It also showed Dr. Weir alone in her office for the duration, until what appears to be Dr. Weir turning into…”

The young woman paused, making a slight expression of distaste as she described the footage. “…a big ball of light with bright tentacles of energy. Or something.”

She waved one hand dismissively. “The event matches every recorded incident of ascension we have in SGC records and which we have found within the Ancient database. Dr. Zelenka was able to successfully open the door approximately thirty minutes ago. At that point, Sgt. Bates and an additional security officer cleared the office and established that it was empty. We have already checked all interior and exterior sensors and there were no ships detected anywhere that could have used any type of beaming technology to remove Dr. Weir from the city. Additional review of security footage also confirms no one accessed the office during the time she was inside.”

Her delicate face firmed with resolve as Miko practically stared down the military officer. “We can not confirm the supposition that Dr. Weir ascended, however, until we have run scans on the room which are most accurate when done as close to the event as possible. We would also like to check her computer and other belongings for any type of note or other indication that she was attempting to ascend or that she had any suspicion that she could or would do so.”

She nodded as if to indicate that she was finished speaking but Radek cleared his throat behind her and she titled her head in his direction. “Of course. There is the additional matter of an energy surge that was detected in the vicinity of the outermost northern tower approximately thirty minutes before Dr. Weir first engaged locks and privacy settings on her office three days ago.”

Sheppard exchanged suspicious glances with McKay and Radek but allowed the woman to finish her succinct but thorough account of the past three days.

“Dr. Zelenka attempted twice in the last two days to schedule a science team to investigate the cause but was unable to get Dr. Weir’s authorization as she did not respond to his attempts to contact her. A security escort would be standard, of course, but such was also denied when Dr. Zelenka requested it to be arranged this morning due to the timing of the event and Dr. Weir’s subsequent behavior. We were told by Sgt. Bates that any such scientific errand would have to wait until the current security threat has been dealt with.”

John managed not to chuckle at the rather adorable scowl that pursed her lips and furrowed her brow as Miko fell silent. He waited a beat to ensure that she was indeed finished with everything she was going to say, then cleared his throat.

“Okay, people. Bates, assign two teams of ten security officers, have one review the security footage for the entire city for the last two weeks and the other is to conduct a thorough sweep of the city to confirm the location and activities of the entire population going back four days.”

The head of security bristled, but nodded sharply and turned on his heel, practically stomping towards the main security office to follow orders. No one said anything as Sheppard faced the Japanese woman. “Dr. Kusanagi, conduct any scans needed to confirm ascension, if possible. Also, you have permission to access Dr. Weir’s office and quarters, including her computer, to check for any evidence to support or disprove what happened this morning.”

As she darted into the office with two other scientists loaded down with various bits of technology both Earth and Ancient, he looked at Radek and Rodney where they were huddled around a console in the control room. It appeared that they were either debating or arguing about the information it was showing them. Probably both.

“McKay, Zelenka, arrange for that trip out to investigate the power surge. We need to know what it was and if it had anything to do with this mess. I’ll get a few Marines to go with you.”

The military commander of the city turned next to the two MPs who had been standing outside the office doors since they had arrived, presumably having been called by the Sargeant before they beamed down.

“As soon as the scans are done, I want you to go through that office like you would a crime scene. If Dr. Kusanagi needs more time with the computer, let her have it, but it stays in the office and one of you keeps an eye on it at all times. It’s to be considered evidence and this is to be treated as a disappearance until we know otherwise. Arrange for however many others you need to conduct interviews with anyone Dr. Weir interacted with in the last two weeks. I want to know everything she did and everywhere she went.”

The two men nodded and turned to watch the scientists, waiting for their turn to enter the office and get to work, one of them reaching up to his ear. John presumed the man was contacting someone to arrange for those interviews but made a mental note to double-check that later. He spared a moment to hope he was making all the correct calls.

If they were on Earth he would have at least had the option of calling an old friend for general advice. As it was, there was no one in the city that was experienced in investigation to at least point him in the right direction. He would just have to do the best he could. With that in mind, he arranged for a team to gear up and walked back over to where Teyla, Ronan, and Caldwell were still standing. The Colonel was obviously speaking to someone from the Daedalus on the radio but he turned his attention to Sheppard as soon as he approached.

“Two of my Lieutenants have MP experience. I’ve sorted them to Atlantis to help with the interviews and any other tasks that are needed. They will beam down in a few minutes and connect with your people. I’ve also arranged for the Daedalus to do a sensor sweep of the city, the surrounding ocean, and the mainland just in case. Is there anything else we can do for you, Colonel?”

“That will be great, though I would appreciate it if one of my officers could go up there and help coordinate the search. There are a few areas that we routinely have trouble with because of equipment that tends to interfere with our sensors.”

Caldwell nodded and relayed the information to his ship while Sheppard arranged for one of the scientists littering the control room to beam up when the former MPs came down. Once that was done, he asked Teyla and Ronon to help the remaining security officers to confine the general populace to their quarters until they knew more about what happened. Then he joined the older man and led him off to the other side of the room where they wouldn’t be easily overheard.

“With Weir gone, leadership should automatically fall to either myself or McKay depending on the situation, but I think it’s safe to say that there might be a bit of ambiguity about whether this is a military situation or not. And I can guarantee that Rodney is not going to want to be in charge. So either way, I anticipate a problem.”

The Commander of the Daedalus inclined his head in agreement. “I’m more than happy to put my weight behind you if it looks like you need to take official leadership of the city. But from what I heard this isn’t a matter of potential threat or imminent danger so you’re right, establishing military control of an officially civilian led expedition without the SGC declaring a change in circumstances would be problematic.”

The two career military men exchanged a silent look that said exactly what they thought of such a change not having been declared as soon as the SGC was informed of the situation with the Wraith. “How certain are you that Dr. McKay will protest his promotion, what is your opinion of forcing the issue, and who would be in line after him if that isn’t an option?”

“Oh I’m positive he’ll protest, loudly and with great vehemence. Forcing him to take even temporary control, while possible, is liable to piss off him and half the civilians, who will have to deal with a pissed off McKay. He’s overworked as it is and simply couldn’t run the sciences and the city at the same time. It would be a bit of a mess and we already have enough of one here to deal with. The next highest-ranking civilian is Dr. Beckett who doesn’t have the fortitude to lead. Bates would run over him like a zamboni. After him is Zelenka who could certainly take control of the sciences short-term but would probably spend all day cursing in Czech if we asked him to do more than that.”

They exchanged another look. The chain of command on the city was not set up for this type of contingency. Caldwell took a deep breath. “Well, if you don’t feel comfortable making the call, I think this situation is enough exigent circumstance to allow for an unscheduled databurst to the SGC. They will no doubt have an opinion on the matter.”

The younger man nodded in agreement. “Until we hear from them, it might be best for Zelenka to take over as acting CSO and for myself and McKay to take official control, maybe if we act jointly it will satisfy enough of the military and civilian members to keep things calm around here. It isn’t strictly in line with the charter though, so I wanted your opinion.”

They both knew of course, that there were a lot of things which in practice did not line up with the charter as far as chain of command on the city was concerned. And it was a concern. Their current circumstances didn’t negate those issues. Caldwell did not voice that, however. He just cocked a brow and spoke with a serious tone.

“For what it’s worth, I agree. The Daedalus will certainly stick around until you hear back. We are already overdue to head back to Earth, though, so I imagine our return will be included in any instructions.”

Sheppard’s face was anything but joyful. “No doubt they will be looking forward to a detailed conversation, face to face, when you get there.”

They both left unsaid that Caldwell may not be the person O’Neill would want to speak with, or that the senior officer may well be the one awarded control if the SGC decided it was time to make the city leadership no longer a civilian post. If nothing else, Weir’s vocal supporters on the IOA would now lack the traction that had previously helped keep her in charge of Atlantis.

They looked over to the gaggle of scientists exiting the office, faces firmly planted in their tablet screens as they walked over to join the two senior scientists. Neither were surprised when McKay came over and informed them grimly that everything pointed to ascension.

“The big question is how. We can’t ignore the timing. If anything caused this, the most likely culprit is whatever also caused the energy surge Radek noted.”

John nodded and called for the Marines, who had just re-entered the ‘Gate room in full gear, to get ready to head out into the city. McKay smirked in satisfaction, then frowned when a soldier picked up his discarded gear and held it out to him.

“It’s not up for debate, Rodney. Get suited up or stay here.” Sheppard felt a small bit of tension that had been knotted between his shoulders for months finally start to release as the other man set down his equipment and did as he was told.

From day one, he had wanted every member of the expedition fully kitted out whenever exploring uncleared sections of the city but had always been overruled by Elizabeth. She had stated repeatedly that there was no hostile threat on the city and that the scientists needed comfort and maneuverability to do their jobs. Despite the circumstances, it was a relief to head out with even McKay and Zelenka outfitted for almost any situation.

Before he led the group of four Marines and two civilians into the far corner of the city, the Lt. Colonel met his superior officer’s gaze. “I don’t feel comfortable delegating this one. Can you take care of informing the folks back home?”

Caldwell smirked. “Yeah, I think I can handle that. Go get us the answers they’re going to be demanding when they call back.”

Sheppard nodded, took a minute to tell Chuck what Caldwell would need while he was gone, then headed out. They hadn’t made it past the edge of the areas cleared for use before the lead scientist was complaining. John made sure not to smile when Rodney grumbled to himself as he tugged at his TAC vest with one hand and fiddled with his tablet with the other. Zelenka rolled his eyes, causing John’s lips to twitch up at the corners. He had been going through the ‘Gate with Rodney long enough that his naturally grumpy behavior was just background noise, which was why the other scientist’s words surprised him.

“Full protocols, yes?”

The CSO missed a step and had to steady himself on the wall when his head turned sharply enough in the Czech’s direction that John was tempted to rub at his own neck. Several expressions flitted across McKay’s face in quick succession. Anger and frustration first. Then a startled look. Then a thoughtful pause that turned to a considering head tilt. Then stark relief. That emotion was brief but it made the Lt. Colonel determined to find out everything possible about ‘full protocols’ because there was definitely a story there he needed to hear.

No sooner had he made the decision than the Chief Scientist bore his familiar self-satisfied expression. Rodney’s normal arrogant confidence was heavy in his voice as he regained his balance and continued down the corridor.

“Yes, yes. Of course. My full protocols, as I originally wrote them. If it’s not broken it doesn’t need fixing, after all. Chop chop people, I haven’t got all day here. Important things to do.”

They all filed down the hall, the geeks cautiously running scans at every intersection and checking something or other on their computers in between. When they reached the lab from which the surge most likely originated, they opened the door, then muttered over their screens for a few minutes before even stepping inside. Then they muttered some more as they looked over the machines and consoles in what appeared to be a lab. Even more muttering and some waving of hands occurred around one large piece of equipment.

“We can interface with the machine without running it, but it will need to be turned on.” Zelenka concluded after a few minutes.

“Yes, yes.” There was some tapping of screens then McKay nodded. “Power has been re-routed from naquadah generator two.”

“We should not step on the platform, I think.”

“Uh, yeah. No stepping on the machine that probably turned Elizabeth into a useless ball of energy. I figured that one out already, thanks.”

John watched the two men squabble, mostly in English, though there was a bit of French and Czech in there as well over the next hour. And a lot of Ancient, at least in writing, which they called a linguist in to translate for them. Before the academics were half way through what seemed to be research notes and data about the machine in question, the CSO turned to his team leader with a sneer.

“It’s a scientific shortcut to ascension. Clever concept, really, but like so many things the Ancients created, it doesn’t seem to have worked out all that well in practice. It was never slotted for general use and while it will take some more time to figure out why, the machine seems to have been mothballed only months after they got it working.”

“Data and experimental findings are transferred to our system. All can be read from elsewhere,” Radek informed them as he unplugged his tablet from the machine and made his way over to them.

“Perfect. I say we take out the power crystal before anyone else around this place gets stupidly suicidal.”

John and Radek both rolled their eyes but didn’t argue as the astrophysicist followed through with his recommendation and carefully pulled a large red crystal from the side of the console and stored it in his pack. No one looked back as they exited the lab and returned to the central tower.

– – – – –

They all gathered in the conference room a few hours after they had beamed down. Two silent moments passed before John realized the senior officer was waiting for him to open the meeting. Clearing his throat briefly, he turned to face the Commander of the Daedalus. “Any idea, sir, how long we have before Earth responds to our databurst?”

Caldwell’s demeanor remained unruffled, but John was pretty sure the older man was laughing at his discomfort as he spoke.

“I imagine once it’s decrypted O’Neill and a few higher ups will have to meet with the IOA before they can reach any official decision regarding Weir and the expedition as a whole. Since you and I are both here, the military command there probably won’t feel naming a replacement leader to be a matter of extreme urgency, so they may wait until the bureaucrats have argued their way through to a solution before issuing any orders.”

The military commander of Atlantis nodded in agreement but knew the delay would only serve them temporarily. The Colonel seemed to agree as he went on.

“That being said, however, when they do make contact, they are all going to expect answers. And not all of them are going to necessarily expect the same answers.” The two military men locked eyes.

“If you are looking for my advice, Sheppard,” John inclined his head, and Caldwell continued, “I would find out as much as possible about what Weir was up to and how she did whatever she did. Make sure you have as many answers to give as possible and make sure that you have as stable a situation here as you can. Any perceived instability or weakness in the running of this city will only increase the likelihood that they will send someone out here to turn this base upside down. I assume you want to stay here, so prove you deserve to before they even think to wonder if someone else would be better in your place.”

The Lt. Colonel took a deep breath and nodded. None of what the older man had to say was a surprise, but it firmly reinforced the tentative plans he had been making. “Right. So, first order of business is figuring out who is technically in charge around here.”

Rodney’s eyes widened and he shook his head sharply when both officers turned to look at him. “Oooh no. No, no, no. I am not being put in charge of these people. It’s hard enough to deal with the idiocy of people with PhDs in fields that matter, there is no way I can handle the level of stupid that makes up the rest of them.”

“Now McKay, you’re the highest ranking civilian on the city-”

“Ha! Exactly. I can’t possibly be expected to run the sciences and the city at the same time. I’m a genius, not a miracle worker.”

The two teammates bickered briefly back and forth – much to the others’ amusement – until John barked out the other man’s name. “McKay!”

Rodney sat up straighter in his chair, opened and closed his mouth twice without saying anything, then slumped forward slightly and glared across the table. Ignoring his friend’s mulish expression, Lt. Col. John Sheppard turned to face the city’s number two scientist. Radek had a resigned but very irritated pout on display.

“This is to be a temporary change, yes?” The words were as much a sharp demand as they were a near pleading question.

“Yes. Until Earth declares an official chain of command for the city, Dr. Zelenka will be the acting CSO with Dr. Kusanagi as his second. Dr. Beckett will remain CMO,” sight of the epic scowl on his friend’s face had John clearing his throat before finishing, “and Dr. McKay will take a joint leadership position.”

Rodney stabbed a finger in the other man’s direction. “It better be joint, Sheppard. I am not dealing with all these useless dumb people on my own.”

Caldwell arched a brow when the younger officer hesitated with a look in his direction. In response, he received an inquiring head tilt in the direction of the room’s far corner. The other brow raised, followed by a nod and the two military men stood and excused themselves for a brief, mostly private conversation.

“Sir,” Sheppard started as soon as they stopped. “I know we had discussed myself and McKay taking over for Weir, but I’ve been thinking. We both know that there are quite a few back home who are waiting for a reason to get rid of me. They already think I can’t follow the chain of command-”

“And you’re worried about their reaction to you placing yourself in a position equal to me.”

John rubbed the back of his neck with a grimace. “Not exactly that. I think the IOA is going to have a problem with the expedition leader and the military commander being the same person. I thought if we at least kept those positions separate we might keep them from coming unglued about it becoming a military operation. But there is no one here qualified to take my spot and if you did so, even temporarily…”

“Ah. You wouldn’t have made yourself equal to me, but placed yourself above a superior officer, thus proving to them that you cannot be trusted to respect the proper chain of command.”

“Which they think already.”

“I see how that might be a problem. I assume you have another idea?” he asked, though they both knew there was only one other option.

“Yes sir. I think you should assume joint command with McKay and I should remain in charge of the military contingent here.”

Caldwell glanced briefly at the sulking physicist, then rubbed a hand over his scalp with a brief grimace. “I agree. Let’s get this settled and start going over what we know so far.”

– – – – –

The military commander looked up from the security team’s preliminary report as McKay and Zelenka finished explaining what they had found in the lab where the energy surge had occurred three days before. Caldwell leaned back in his chair and cocked an eyebrow at the younger soldier. “So we know that the machine was used and that it was designed to speed up the physical process of ascension. Can we prove that Dr. Weir herself used it?”

“The security footage from the last few days has been partially reviewed. I had them focus on Weir’s movements first,” Sheppard answered, glancing back down at the report before continuing.

“She is clearly shown passing the limit of the security perimeter and walking down the hallway that leads towards the lab about twenty minutes before the energy surge. She remains outside the range of our security cameras during the time the surge from the machine registered on the sensors. No one else was noted outside the security perimeter that we can find. We do have footage of her coming back into camera range about twenty-five minutes after the surge looking very pleased with herself and going straight to her office. Records show she locked the door, set the privacy, and stayed inside the entire day.”

The older man appeared to consider that for a moment in silence before he responded. “The logs show her leaving for over an hour that night, correct?”

John nodded. “Based on the footage, she let herself into the storage room allotted to the mess and commandeered about two weeks worth of rations. She appears to take the boxes of food back to her office where she locks herself in, cancels all meetings, and works almost nonstop on her computer until she turns into a bright ball of… whatever.”

“She doesn’t do anything other than work on the computer?” the new co-leader of Atlantis asked.

“Well, sir, she walks around the office a little. And she eats. A lot.”

“What I’ve read of the data on the machine indicates increased appetite is a standard side effect of the genetic alterations forced by the machine,” interjected Rodney, though he didn’t look up from his own tablet as he did so.

“And she stocked up on food less than a day after using the machine.” John said, thinking it over before looking up at the others. “So we can assume she expected the need to eat a lot and therefore probably knew what the machine would do before she used it.”

“All indications point that direction, Colonel,” Radek answered. “But since she does not get herself enough to eat until after using the machine it is possible that she read about it afterwards. We will not be sure what she knew, when, until we can examine her computer.”

All eyes turned to the petite Japanese scientist sitting straight in her chair with both hands folded neatly on the table in front of her.

“Unfortunately, we have had limited success so far in accessing Dr. Weir’s computer. Other than her email, almost everything on the computer is either password protected or encrypted with varying degrees of complexity. We have, of course, gotten through the passwords but the rest is proving difficult.”

Both soldiers and the other two scientists stared in silence for a moment. Some files being password protected was not out of the ordinary for someone with her position. But encryption was not something they would have expected to find.

Rodney scowled. “What kind of encryption are we talking about here?”

Miko nodded towards the former CSO’s tablet. “I sent you examples of some of the coding. Older files and folders should be fairly simple for me to get into, though it will take me some time to hack in. The newer folders, however…”

McKay made a choking sound as he scanned through the email. “What the hell is this? Is this Ancient coding? How the hell did someone with a Political Science degree manage this level of encryption?”

The young woman nodded and faced the other temporary expedition leader. “I do not know at this point how long it will take to get into the files she saved after using the machine. It would seem that in addition to increased appetite, one of the side effects is a startling increase in intelligence and technical aptitude.”

“Uh, yeah! No way Elizabeth could do this without ascension-brain. I want this decrypted, Kusanagi. Pick a couple minions and get to work, some of them can manage the earlier stuff. Send me…” Rodney trailed off with a thunderous expression. “I’ll be busy placating truly stupid people but I will grab a bit of code to go over when I can. Assume you’ll be handling the later, Ancient-y bits yourself.”

She nodded gracefully while he slumped back in his seat and crossed both arms over his chest. Radek seemed to ignore his boss’s petulant huff beside him and spoke up.

“On positive side, we were able to turn off all command codes that had been assigned to Dr. Weir in our systems and alter all others she was aware of.”

Rodney rolled his eyes. “Oh boy. That’s great, seeing as she’s a big ball of shiny tentacles content to watch people actually live their lives and not interfere in the goings on of us mere mortals. I’m sure her access to our computers was a real threat.”

Zelenka paused until the rant had completed then picked back up as if he had never been interrupted in the first place. “You will all receive updated codes within the hour.”

“Thank you, doctors. Until we know more from the computer I would like the physical search of her office to continue,” Caldwell glanced at the military commander, “I trust the MPs still have not found anything of note?”

“No sir.”

“Very well. Then I believe the main focus before we hear from the SGC should be the security footage. I want to see where she went and how often, and for how long she had been doing so.”

Sheppard nodded, then looked at the acting CSO when he spoke up. “Uh, we could help there, I believe, Colonel. If we write program, it could go through all the footage and isolate any sightings of Dr. Weir. Otherwise, there could be far too much to go through, city-wide.”

“That’d be great, doc,” John stated as he looked to Caldwell for the go ahead. Receiving a nod and the slightest hint of a smirk from the senior officer, he waved a hand at the Czech scientist. “Get whoever you need on that as soon as you can.”

“Yes, yes. I will do so.” Radek looked expectantly around the table. “I can do that now, yes?”

“Yeah Radek. Go, both of you.”

Miko stood and nodded at the co-leaders, pausing before she followed her new CSO from the room. “I will send updates to you both every four hours to inform you of our progress with Dr. Weir’s computer.”

Once the two had gone, the doors all swung shut once more and Sheppard faced his superior officer. “Why do I get the feeling you’re really enjoying being in my direct chain of command?”

The Colonel smirked just a little. McKay shook his head with an exclamation of, “Ha! Who wouldn’t revel just a little in being able to order around mister fly-by-the-seat-of-his-pants, never-think-things-through-before-rushing-off-into-danger. I certainly plan to. Oh! I get to boss you around now! Wow. Maybe this won’t be so bad after all.”

Rodney stood and turned to go, then stopped in his tracks. “Oh who am I kidding, this is going to suck. And it’s all your fault, Sheppard!”

John raised both hands in surrender when the scientist jabbed a finger towards him and spun back around. “Come on Caldwell, I’m not dealing with these idiots by myself.”

The older man still looked to be smirking when he trailed behind the irate physicist towards the control room.

– – – – –

Sheppard couldn’t suppress a sigh as he dropped into the chair in the office space they were using for the temporary expedition leaders while Weir’s office was gone through with a fine-tooth evidentiary comb. He knew he wasn’t alone in his distaste for meetings, the tired scowl on Caldwell’s face and the angry pout on McKay’s was proof enough of that. But as the alternative was reading through yet more reports on this whole mess, they had decided to get together for a quick talk before they set about writing their updated status report for the expected dial-in from Earth.

John almost sighed again at the thought. They had been waiting less than comfortably for a response to their databurst for more than twenty-four hours now. Since it was probable that the SGC had now had enough time to convene the IOA and agree on a course of action, they could be receiving orders at any time. They hoped to have as much ready to send back as possible. Which meant keeping each other up to date on the various avenues of their investigation.

Miko cleared her throat as she took her own seat, calmly folding her hands on top of her tablet. She was the only one at the table with an unruffled expression. “The keyword search programs I wrote to help us go through Dr. Weir’s computer have proven successful; at least with those areas we have gained access to. As you know, the older files have been decrypted for several hours and the search program has painted a fairly clear picture despite the fact that we have not yet been able to spare the time to read through all the decrypted information.”

The young woman didn’t even fidget as she went through her oral report. “There are quite a few documents and files concerning ascension which, based on the dates, were on the computer when we came to Pegasus. Many more files were added, and password protected, approximately a week after we arrived. The first ones accessed, appear to be those related to the energy creature the Ancients trapped to study.”

“That was our first indication that they studied ascension scientifically,” the former CSO pointed out.

John nodded, remembering somewhat vaguely that Rodney had said something similar at the time. Elizabeth had, on reflection, been quite excited by the news.

Kusanagi nodded politely to indicate agreement but continued as if no one had spoken. “They were opened repeatedly for the first few months. The second set of files that appear to have been opened and subsequently locked by Dr. Weir, were downloaded to her computer about three months after our arrival. They are all concerned with the topic of Ancient memory storage devices, namely memory crystals.”

The others frowned but any confusion evident shifted to variations of anger or frustration when the Japanese woman reached into a bag next to her and removed a clear-sided containment box. When it was placed on the table between them it was clear that it housed a single large yellowish crystal that looked like a cross between Ancient and Goa’uld power crystals.

“This was found during the search of Dr. Weir’s office. At the time, we were unsure what it was or why it was locked in a hidden compartment inside a cabinet.”

“And now?” John asked through clenched teeth.

“Further examinations of the crystal itself, and the unlocked files, has led us to believe it is a crystalline structure the Ancients used exclusively for data storage. There is a device to read the crystal in a lab at the far end of the north-west pier.”

Rodney narrowed his eyes. “How do we know that? That section has not been cleared for even cursory exploration by the Marines or the science department.”

“The lab with the device was accessed by Weir less than four months after we came to Pegasus. It was the first such uncleared lab we have evidence of her accessing.”

“But obviously not the last,” cut in the co-leader. Caldwell frowned for several moments at the crystal, then fixed the scientist with a neutral stare. “How many labs and areas do we have evidence of her accessing which she was either unauthorized to open or which had not been cleared for use?”

“At this point, three. The lab with the data-reader, a room which so far appears to be a secondary access point for the Ancient database, and the lab in which the so-called ascension machine is housed. As we have only begun to examine both her personal files and the security footage, I believe it very likely that we will find evidence of a large number of similar locations.”

While McKay stood from the table with a huff to refill his coffee, John ran a hand over his face trying to process the possible scope of Elizabeth’s actions. Some of the labs and areas of the city which had been declared off limits to personnel had been given that designation because they housed known threats, such as the lab where the nanite bioweapon had been found. If she routinely accessed unknown or out-of-bounds areas they were probably quite lucky she had not endangered the entire city more than once. For all they knew, she had endangered the entire city more than once.

The sharp clink of his friend’s mug hitting the desk broke him from his thoughts, though the expression on Rodney’s face told him they had both been contemplating the same topic. “Where did she get the crystal? Do we know yet?”

Miko inclined her head. “Indeed we do, Dr. McKay. One of the things we found on her computer which we have been able to gain access to, has been what amounts to a personal diary. In several of the entries we have listened to, she references a ‘beautiful gift’ which was given to her by the elderly version of Dr. Weir we found in the stasis pod last year. Another entry describes this gift with a great many descriptive phrases, including ‘golden crystal.’ I am confident that she was referencing the memory storage crystal we found.”

“So Old Weir gave her information about what, ascension?”

“Based on diary entries where she discusses the ‘knowledge granted through time’ we can assume most of the crystal’s content has to do with ascension.”

The astrophysicist made a face at the phrase, and John had to swallow back a snort of laughter. Apparently Elizabeth had been more poetic than he had known. If that example was an indication of her personal writing on the whole, she seemed to tend towards bad poetry, but poetry all the same. The crinkled brow on Miko’s face seemed to say she found the wording of similar literary value as she went on.

“In addition to ascension, there are what appear to be files regarding the ATA gene.” The young woman opened a file on her tablet to show McKay.

Rodney stared at the screen, eyes darting back and forth as he read. John leaned over, half in the other man’s lap in order to see for himself. The former CSO huffed but leaned back for almost a minute, no doubt rolling his eyes the whole time. After about sixty seconds, he seemed to loose patience and shoved at Sheppard’s shoulder to move him out of his way. John straightened in his chair, having seen enough to get an idea of what they’d found.

“So that’s why she insisted on being given Carson’s therapy a second time about four months after we got here.”

“And why it worked when all his research and the first failed attempt said it shouldn’t have.” Rodney crossed his arms over his chest, looking half furious with her actions and half satisfied, no doubt relieved to have the statistical anomaly finally explained.

John shook his head at his teammate’s contradictory behavior, giving himself a moment to think over everything. It was infuriating that without her older self’s interference Weir would never have known what to look for or had a working ATA gene to operate anything in the city she had wanted. “Fuck.”

“That about sums it up,” McKay agreed before taking a long drink of his coffee.

John rubbed the back of his neck and resisted the urge to sigh. “Anything else on that thing we should know about?”

Miko closed her tablet and set it neatly in front of her once more. “Until we have cleared the lab and can use the data-reader ourselves, or can find a full transcript of the crystal’s contents, we will not know for sure.”

“There isn’t a transcript on Weir’s computer?”

She shook her head at the former CSO’s question. “Not yet, just her notes. We have only managed to open a small percentage of the files and of those opened, much of their contents have not been examined. It is entirely possibly we will find it. Dr. Weir seems to have stored a great number of files, some compressed by fairly advanced algorithms, so the chances of her not retaining a copy are slim. Even so, I would recommend we acquire an original copy for our own records in case there was anything on the crystal she did not feel it was important to save.”

Caldwell nodded, a short hand gesture silently giving his permission for the computer scientist to go ahead with that plan. “And the diary you mentioned? Does it give us any clear indication of Dr. Weir’s plans regarding what happened to her? Can we say, without a doubt, that she purposely used the machine on herself with the intention of ascending?”

“According to the earlier entries, Elizabeth came to Pegasus with clear plans to research ascension with the ideal end result of ascending herself. The appeal it held for her is not subtle. Entries after the city’s self-destruct was almost used are filled with the impression she thought time was running out for her to achieve her goal. Other factors are also evident in later entries.”

The Colonel cocked a single brow when he found himself the focus of Miko’s gaze.

“I find myself curious, Dr. Kusanagi. Can you play one of the entries for us?”

“Of course, sir.”

She re-opened her tablet, then situated it in the middle of the table before tapping on the screen several times. Elizabeth Weir’s voice immediately filled the conference room.

I don’t know why I thought I would be happy when we regained contact with Earth. It has been more trouble than it is worth. Granted, the ZPM will make many of my plans move more easily and more quickly, but the dangers have increased so much. The military structure of the SGC got in the way so many times during my early research. I was so sure that with the expedition clearly established as civilian-led that such things would be over.

There was a rhythmic sound behind her words, as if she were drumming her fingers against something or perhaps tapping a stylus against her desk with a good deal of force. It emphasized the frustration in her voice as she continued.

I am in charge here. I’ve put in way too much effort to make that position clear and safe after Marshal went and got himself killed. But now they keep sending more military thugs out here to ruin it all for me. Everett was bad enough, trying to take over my city, issuing commands to my people as if he had a right. Trying to leave me out of meetings to decide the fate of my city. But Caldwell…

She let out a noise that was so similar to what he had once heard on a documentary about badgers that John had to cover his mouth to keep from laughing. The rant that followed varied in tone and volume but was filled to the brim with negative views on Caldwell and Sheppard and the challenge they posed to her stranglehold on power in the city.

I have worked too hard! I sacrificed for years to get here. I traveled through time to get this far! I can’t let them destroy everything I have accomplished. I won’t let them keep me from reaching my full potential. I deserve a higher existence than this. I deserve the universe to explore and experience as the Ancients did. Just because my gene isn’t natural doesn’t mean I am entitled to less of this city than the likes of Sheppard. Ascension is possible here. It’s waiting for me somewhere in this city, I know it. I’ll find it.

“So,” McKay asked, breaking the silence that had descended on the conference room as the recording ended, “how exactly did we all miss that Elizabeth was, you know… completely nuts?”

John just shook his head without responding. He truly did not have an answer to that question. Less than an hour later, after Atlantis finally received an answering databurst from the SGC, he resolved to give it some serious thought. General O’Neill would certainly want to know how none of them had ever seen evidence of what Weir had been up to. And he would soon be in a position to give what he hoped would be a semi-coherent response to that and many, many other questions. In person.

Lt. Colonel John Sheppard had been recalled to Earth to be officially debriefed by the SGC and the IOA.

Chapter Two

He had never ostensibly flown an aircraft without actually piloting it. Sitting in the commander’s chair on the deck of the Daedalus, technically at the helm without actually doing anything other than giving the occasional order for the crew to do things they already knew they needed to do was more than a little surreal; and a whole lot uncomfortable.

As much as he was not looking forward to the interrogations awaiting him at the SGC, John couldn’t wait to get this trip over with. It had been about a week since he had left Atlantis and today marked their last day in the Pegasus galaxy. Which meant it was his last chance to receive any reports from the city about the ongoing investigation into Weir’s actions. Seeing as he would be expected to account for those actions and explain to the pencil pushers on the IOA why their golden girl had floated off into the metaphysical sunset, he was keeping an eye out for the transmission.

He didn’t have to wait long. Before his shift on the bridge even finished, he was informed that a databurst had come through and that it would be waiting for him on the computer he was using in his temporary quarters. John spared a moment to wish, yet again, that he could have sent Caldwell back to earth with the reports and stayed on the city himself. But the orders from the SGC had left no doubt how much O’Neill and the IOA wanted to speak to him personally, and how soon they expected the Daedalus back in the Milky Way.

So, Caldwell was cleaning up Weir’s mess in Atlantis, and John was given temporary command of the ship for the trip to Earth where he would bring that mess to the bureaucrats. What fun. Sheppard ran a hand over his face and turned on the computer without actually sitting down at the desk. He had done enough sitting on the bridge and he would spare his ass the additional abuse by reading on his feet.

By the time he was half way through the transmission his feet ached and sensation had returned to his ass. He sat on the edge of his bunk with a groan. Based on the number of files Miko’s team had unlocked and decrypted so far – less than half of what had been on Weir’s computer – the former leader of the Atlantis expedition had obviously had way too much time on her hands.

“What the hell did she do on the city?” he muttered to himself as he rubbed his eyes and tried to talk himself into reading the rest of what Caldwell and McKay had sent him. When he finally managed it, John made sure to situate himself more comfortably as he had no doubt what he would be doing the next few hours, at least.

Reading through the findings – which clearly detailed Elizabeth Weir’s obsession with ascension and the Ancients in general – was hardly a surprise by any stretch, but it was still a less than pleasant way to spend two and a half hours. The additional copies of files that had been successfully accessed on the woman’s computer, however, were somehow worse.

When he got to the drafts she had made of treaties for them to use with the Genii and even the Wraith, he had to set his tablet aside and pace off some of his anger. He wanted to scream, to rage, to bitch and moan. If he had been on the city he probably would have. Especially if Rodney had been around. Rodney was by far the best bitching companion he had ever had. At least he was when the scientist let him get a word in edgewise. Though even just listening to McKay complain without being able to contribute himself somehow still managed to help him burn off his own frustration by proxy.

What he would give for that outlet now, John thought as he gripped his hair tightly in both fists. The idea that she apparently still thought they could negotiate and work with the Genii after all the times they had double-crossed and outright attacked them was mind-boggling. And the Wraith… The Lt. Colonel collapsed back onto the bunk.

“Fuck,” he cursed under his breath. How could even a naive academic with a degree in Political Science have lived in Pegasus for almost two years and still somehow operate under the delusion that they could form a treaty with a race that ate them? How the hell did you negotiate with that?

He shook his head, eyes straying back to the tablet and the files it still displayed. Sure, he thought, he’d had his share of problems with her over the length of the expedition. He certainly hadn’t trusted her, but until McKay had said it in the conference room the week before, he’d never thought she was actually insane.

Sheppard covered his face with both hands at the thought of the meetings that awaited him at Stargate Command. He’d rather be attempting to negotiate with a Wraith. At least then he would have the option of settling the matter with his P-90.

– – – – –

None of the information he presented during the first half dozen meetings was well received by the IOA. Some members, who had previously spoken quite forcefully about Weir’s inclusion in the expedition and her status as leader, appeared personally insulted by the factual recitation he had made thus far. John did his best to keep his opinion to himself in every way, but he figured by the look on O’Neill’s face that the General had a pretty good idea what he thought.

John had a pretty good idea that O’Neill agreed.

“So, you’re saying that Dr. Weir was able to circumvent the military perimeter you had set up on the city and access at least seven un-cleared or out-of-bounds areas without a single person on your security team being aware?” Woolsey asked in a rather snide tone. “And she also accessed the Ancient database dozens of times without the science department ever detecting it?”

Woolsey seemed to have been elected the IOA spokesperson. Judging from the way the bureaucrat was flipping confidently through the reports that had been sent ahead of him, however, the soldier thought that position had more to do with the fact that Woolsey was the only one that had read all the reports. The mousey looking man seemed inordinately comfortable with all the official paperwork stacked up in various tidy piles on the table in front of him.

John clasped his hands a little tighter where they rested on the table but otherwise gave no indication of being bothered by the repetitive and insulting questions he had been answering for the last couple days.

“As the leader of the expedition, Dr. Weir was given copies of all security schedules and guard positions. As an intelligent woman I am sure she was able to plan her unauthorized trips accordingly.” Sheppard knew better than to mention that having Bates as head of security allowed her even more access to such things than she was entitled to because of her position.

“The Ancient database, as I am sure you remember from our reports, is notoriously difficult to navigate. Our techs are still trying to set up a system that will allow them to find vital information in it, let alone track access. Monitoring such a thing has never been high enough priority to reach the top of their list since we believed there was only the one access port into the database, and it was monitored externally by the security teams.”

The Lt. Colonel, took a short sip of water before fixing the various members of the IOA with an almost sincere smile.

“I am sure that will be easily dealt with now that we know there is another port Dr. Weir neglected to mention finding. The organization pattern she was able to decipher within the database will also make a large difference in our use of it now that it has been decrypted off her computer.”

Woolsey cleared his throat and several other IOA members shifted in their seats. There was a long enough pause before the Board fielded another barbed question for the General to cut in and call for a lunch break. The bureaucrats slowly, grudgingly, filed out of the room until only Sheppard and O’Neill were left.

John had joined the expedition so late that he had never really gotten a chance to serve under the General before they went through the ‘Gate. So he eyed him somewhat wearily as the older man sprawled in a chair on the other side of the table and eyed him right back in a very un-subtle way. The younger man made an effort to remain still and outwardly calm but it was rather nerve-wracking not knowing what to expect from the superior officer.

All John Sheppard knew about General Jack O’Neill was that the man thought he had flown well avoiding the drone at the outpost, and that he had warned Weir that John didn’t respect the chain of command. Caldwell had responded well to his rundown of the situation on Atlantis back when he had taken temporary command while John turned into a bug. But the Lt. Colonel had no idea how O’Neill would react to the full report he had sent ahead for the General’s eyes-only.

It didn’t appear that he would have any immediate answers to that, as the former leader of SG1 finally spoke with an almost dismissive wave at the now-empty seats.

“They’re rather annoyed about all that evidence you have of her joining the expedition and lobbying for her leadership position for the sole purpose of finding a way to ascend. They would have much preferred it if they could argue that all of her problems manifested on the other side of the Gate.”

Sheppard sighed, understanding what wasn’t being said. “That way they don’t have to find a way to justify having placed an ascension obsessed, possibly suicidal, crazy person in charge of the entire expedition against the express wishes of the majority of those in charge of the SGC.”

Jack let out a short laugh. “You bet’cha”

An awkward silence fell between the two Air Force officers and lasted at least a dozen very long seconds before O’Neill sat up straight, placed both hands on the table, and fixed the Atlantis military commander with a narrow-eyed gaze.

“Now, we both know that the pencil pushers need their questions answered, their papers filed, and their asses covered. But we also know that they forced the issue with Weir’s placement and it’s come back to bite them. So the assignment of the new expedition leader is going to be my decision, I have Hammond’s word on it. I have the president’s word on it, and not even the IOA is going to have a damn thing to say about it. But before I can make that decision you and I need to have a conversation, wouldn’t you say?”

John, having lectured himself severely for a good portion of the mind numbing hours he had spent in Caldwell’s chair on the Daedalus, was able to keep his face completely blank and respond with a respectful, “Yes, sir.”

O’Neill’s eyes narrowed a bit more, then he nodded once to himself and leaned back into his chair. “Good. Walter and Mitchell have been tasked with keeping the IOA busy for the next couple hours so it’s just going to be you, me, and a very interesting report Caldwell sent in the last databurst before Weir decided to go bright, shiny, and non-interference on us.”

It was John’s turn to give one sharp nod, though he remained stiff-backed in his chair. “I assumed he had, sir.”

With that, the very uncomfortable military debrief began. They talked about Weir, then Sumner, then Weir again. Then they moved on to John himself, then back to Weir. After that, they discussed Bates and more about Weir, and finally moved on to Beckett, though that topic had quite a bit to do with Weir, and Sheppard too. And Iratus. Mustn’t forget the Iratus.

“So, you were a big blue bug, huh?”

“Yes, sir. The retrovirus infected me rather thoroughly, sir,” was John’s careful response.

“And now?”

“Sir?”

“That drug changed your DNA, Sheppard. Beckett’s report of the incident indicated that you had returned to normal but did not include much in the way of concrete DNA results to back it up and Caldwell’s updated report says you’ve seemed a little different to him since. More serious, more strategic, less tolerant of certain things.”

John took a deep breath. “Permission to speak freely, sir?”

O’Neill made a ‘go ahead’ motion with the sweep of one hand and appeared to get comfortable in his chair.

“The Wraith make me… itch, sir. Just the thought of them sometimes, makes me hyper-focused, and I feel, well, it’s kind of like the adrenal response I had before, when…”

“You were a big blue bug?”

He let out a huff of breath. “Yes, sir. Something like that. When we were going to meet the Aurora, I was very… aware of our location and twice had the urge to run additional scans to ensure there were no Wraith nearby. That they weren’t… shit, sir. I wanted to make sure they hadn’t encroached, so to say. On my territory.”

Both of Jack’s brows rose in surprise and the younger man let out another breath, rubbing a hand over his face briefly before meeting his gaze.

“It sounds really bad when I say it like that, doesn’t it?”

“Well, it sounds like something. How else would you compare how you’ve felt since the infection with how you felt during the infection?”

John swallowed, but while the General sounded very serious, he seemed more curious than suspicious so he hoped that meant he wasn’t about to be thrown into a dark hole for everyone else’s safety. Or worse, to be the subject of some black-site experimentation.

“At the time, I remember feeling aggressive more than anything else. I was extra aware of my surroundings, leery of any perceived threat, all of which made me feel even more aggressive and prone to attacking that threat in whatever manner I could.”

John resisted the urge to rub the back of his neck. “But I haven’t felt aggressive like that since. I felt more on-guard around Weir, like I was preparing for some kind of retaliation, but I think that had more to do with the fact that she was smart enough to realize Caldwell had helped me do an end-run around her to get those changes made while he was temporary military commander. Other than that, the only threat I have perceived is that of the Wraith and frankly, sir, I would worry a lot more if I wasn’t more focused on those things after getting up close and personal with the creature they were made from.”

O’Neill tilted his head forward – hopefully to acknowledge that point – but didn’t interrupt, so John continued.

“I think I might have a small insight into them now, the way they perceive and react to threats and how we might use that to our advantage. I wasn’t aware that I was acting more… I think you said Caldwell called me strategic?”

Another nod.

“Well, I don’t know about that but I have spent more time thinking about our military position out there and after those improvements were pushed through, I have been considering other changes I had wanted to make, ways I can strengthen our stance in Pegasus and better fortify the city. As for being less tolerant, well sir, I’m not entirely sure what he meant by that.”

“Well, Sheppard, it seems you’ve been keeping a very wary eye on a few people on the city. Steven wasn’t entirely sure of your reasoning, but he made a few guesses.”

“Oh. Well. I know I was watching Weir, but like I said I think it had more to do with her reaction to Caldwell’s temporary stint as military commander than anything else. Though I admit a lack of trust there was inevitable after our time on the city.”

Neither officer wasted time going back over all the problems that they had already discussed in that vein, allowing the man to finish what he was saying.

“I may have also been more… vigilant, lately. Around my team. I don’t know how much that has to do with anything. I think, sir, it’s mostly because of the mess with Ford and having to step down as military commander and give the position to someone else. I trusted Col. Caldwell to do right by Atlantis, but it was hard… admitting I was a liability to them. Re-assuming my duties was a relief and I did so with the intention of taking a firmer stance on what I did and didn’t allow from my men and from the leader of the expedition.”

“I see. That explains most of what Steven observed, I think.” The tone was curiously satisfied, almost proud, and John again fought the urge to rub the back of his neck as he sat under the heavy gaze of the battle-hardened officer. “Other than the good doctor, of course.”

“Sir?”

“Beckett. You’ve apparently been giving Beckett a bit of the stink-eye since your pyscho-Smurf impersonation.”

“Ah. Well. Sir…”

“Spit it out, Sheppard. Speak freely and all that.”

“Yes sir. I have some… questions, about a few of Dr. Beckett’s projects. I would rather have some concrete data before bringing it up. Officially. But I didn’t have authorization to view any of the research proposals or plans or findings. It is my understanding that Dr. Weir gave him the go ahead for his personal research projects rather than him going through the CSO as the charter states.”

“And unofficially? Have you talked about this with McKay?”

“Briefly. Long enough to know that he wasn’t aware that the ATA treatment hadn’t gone through human testing until Beckett was injecting him with it.”

“Pardon?”

“Things were very chaotic the first few weeks. Space vampires was not exactly what we were expecting to find when we arrived and once we found our feet, Weir had already cut the both of us off at the knees and we didn’t even realize it. Now that those things are being restructured, he’s been a little busy with administrative duties. I had hoped to get into it after the Weir situation has been dissected and contained.”

It went unsaid that his return to Pegasus – let alone his position once he got there and therefore his ability to do that – had not been officially decided.

O’Neill just nodded. Again. “Very well. I expect the military commander of Atlantis and the new expedition leader will both look into the matter and report back to me so any decisions or changes can be made if necessary.”

John took a page out of his superior’s handbook and nodded silently, mentally preparing himself to be dismissed or tossed back to the IOA sharks for the remainder of the day. Neither of those things happened, however, and a strained silence filled the room. Sheppard swallowed back the smart-ass remark floating in the back of his head, determined to show his CO that he was capable of being a good solider and following the chain of command without argument.

The General’s next words tested that resolve to the utmost.

“So. Afghanistan.”

“Sir,” Sheppard replied as neutrally as possible to the ominous non sequitur. Any mention of the clusterfuck that had resulted in his black mark three years before tended to put him on the defensive. His CO mentioning it, especially when his place on the Atlantis mission was in doubt, left him positively uncomfortable.

“I glanced through your file after you sat in the chair and I admit, I wasn’t thrilled with your placement when the expedition left. But I figured Marshal Sumner was a militant enough bastard to keep you in line and your gene was valuable to the mission. Then I heard Sumner was dead and Weir had not only put you in his place, but promoted you on top of it.”

There was absolutely nothing John could think to say so he kept his mouth shut and let his superior officer say whatever he was going to say.

“When we got the first databurst you could say I was prepared to regret my decision. Nothing had gone catastrophic with you in charge, though, so I waited until I could review the entire situation. Everett’s report upon his return was certainly a mark in your favor. A surprising one. Then I got Caldwell’s report and I was… flummoxed.”

Sheppard blinked, suddenly unsure where this was headed.

“So while you were on your way back here, I did some digging. And I came across a report that I found quite surprising. Almost as surprising as the formal decision passed down from JAG only a few months ago that I also happened to give a look-see. I made a few phone calls, the content of which frankly pissed me off quite a lot. Then I made a few decisions of my own and generally stuck my nose in a few places it wasn’t wanted and ruffled a few feathers.”

John had absolutely no idea how to respond to that. Confusion was becoming something of a watchword since his conversation with O’Neill had begun. A little self-satisfied smile on the older man’s face insinuated that he was aware of the effect he was having and was quite enjoying it.

“The end result of the last two and a half weeks is as follows. Colonel Millnis has retired from the Air Force and Lt. Holland has been posthumously awarded the Air Force Cross and the black mark on your record has been officially, but quietly, expunged.”

The younger officer sat in silence. He wanted to speak. In fact, he had quite a few things to say, but none of them would come out of his mouth. After a few moments he simply nodded and received the same gesture from O’Neill.

“All righty,” the General suddenly stated as he slapped both hands on the table and stood. “Now that all that’s out of the way.”

O’Neill walked over to the wall and picked up the phone mounted there. “Walter, how about some coffee. Oh and send the vultures back this way.”

John couldn’t hear the response but the older man nodded and hung up the phone as his gaze shifted to the door, clapping his hands together once as he rocked on his feet and completely ignored the younger officer behind him. A moment later, the door opened just long enough for a tray to be handed through. The General brought it to the table and poured himself a fresh mug of coffee with patient movements. John finally shifted uneasily in his seat.

As if he had been waiting for the indication of the younger man’s discomfort, Jack finally set down his steaming mug and got comfortable in his seat once again. “Go ahead and get yourself another cup, Colonel, the IOA are on their way back in. It’s time to wrap this up.”

– – – – –

John Sheppard toyed absently with the silver oak leaves on his collar while his eyes flicked back and forth from his computer screen to the telephone in his temporary quarters inside the Mountain. The expressions on the IOA members faces when it had been made clear that Colonel Steven Caldwell would be given the official leadership role on Atlantis, effective immediately, and that Lt. Col. John Sheppard would retain command of the military on the city had been quite amusing.

John wasn’t sure why the pug-nosed US rep on the Board had been quite so put out at the idea that Caldwell would not be returning to Earth anytime soon or that Ellis had been given command of the Daedalus and was already onboard the ship, getting it restocked for the trip back out to Pegasus. But the man certainly had acted frustrated and rather pissed at both facts. Then again, none of the pencil pushers had looked particularly thrilled with how things had ended up.

Dismissing the matter, he closed his laptop and eyed the phone again. He’d been told only an hour before that he was on leave now that the debriefs had finished. He was free to leave the base if he wanted as long as he was back in time to depart on the Daedalus in two weeks time. Which gave him plenty of time and opportunity to make the call he had been avoiding.

“Fuck it,” he muttered, reaching for the phone before he talked himself out of it. The number was quickly dialed, still fresh in his memory even after nearly a decade of not using it. There was a brief moment of doubt, of concern that the office number had been changed, but then the call connected.

“Sheppard Industries, Patrick Sheppard’s office.”

John cleared his throat. “Yes. Uh, is Mr. Sheppard in?”

“I’m sorry, he’s not in the office today. Can I take a message?”

“Oh, uh. Sure. I guess.”

“And what was your name, sir?”

“Oh, right. Lt. Col. John Sheppard. I have a number I can leave, but I’ll be back in the field in a couple weeks so, it won’t be good then. How long do you expect him to be out of the office?”

“I’m sorry sir, did you say John Sheppard?”

“Yes ma’am.”

“Mr. Sheppard’s son, John?”

“Yes ma’am.”

“I’m sorry, could you hold a moment, please?”

“Uh. Sure.” John pulled the phone away from his ear and looked at it as Mozart started to play over the receiver. He put it back a moment later when the music stopped and another voice replaced it. A very familiar voice.

“John?”

“Dave. Hey. How are you?” The officer cringed at his ridiculous attempt at being casual.

“Seriously, John? What the hell? Where have you been? Where are you?”

He sighed loudly enough that he was sure his little brother was gnashing his teeth. “Sorry. I, well, I’ve been on a classified project for a bit. I’m in Colorado now and I thought, maybe, well… shit Dave. I don’t know. This was obviously a bad idea.”

“No, John, joining the Air Force because you fought with Dad over what you were going to major in at school was a bad idea. Refusing to consider what he wanted for your future and instead risking your life to fly helicopters was a bad idea. Sending that fucking goodbye message after ignoring every call and email for a year and then dropping off the edge of the fucking planet afterwards was a goddamn colossal fuckup.”

The elder Sheppard brother took another deep breath, reminding himself that he had decided during the siege that he would make a concerted effort to patch things up with his family if he ever got a chance. Hanging up now would leave them exactly where they had been when he left Earth. Angry and silent. Sheppard men did angry and silent very well. It was time to try something different. Maybe. If he could hold his temper.

“Damn it John.”

There was silence for several seconds. Gathering what determination and civility he could, he tried to keep his voice calm. “Look, Dave. I’m on leave for the next two weeks, I thought maybe we could grab lunch or something.”

The younger brother let out something between a huff and a grunt. “Where in Colorado are you? I’ll send the plane to pick you up.”

“You don’t need to… I can take a military transport, Dave, it’s not-”

“Fuck you. What’s the closest air strip?”

He closed his eyes for a moment, then rattled off the information his brother was asking for. He had meant what he said in the video he’d sent from Atlantis. He regretted the way he’d left things with his little brother and he did want to do better. But damn, he’d forgotten how hard it was to deal with the sanctimonious brat.

– – – – –

He wasn’t surprised to see Dave waiting for him when the plane landed, but the greeting was certainly unexpected.

“Look, I’m sorry I brought up all that crap on the phone. I was surprised you called and I’ve been pretty pissed because we couldn’t track you down and… Any way,” David admitted as he rubbed at the back of his neck the same way their father did when he was uncomfortable, “I told myself I wouldn’t dredge up the past when I finally got to talk to you, so, sorry.”

“Uh, yeah. It’s fine. In the past, blah blah blah.”

The younger brother rolled his eyes and just motioned him into the car that was waiting to take them to meet their father for dinner. Hearing their destination left a knot forming in John’s stomach despite having been pretty sure that was where he would end up that night. The ride was longer than he remembered, and full of stilted small talk. But nothing was as awkward as stepping through the front door to see his father standing there in a pair of slacks and a polo shirt, expression painfully blank.

“John,” the older man said in a neutral tone that perfectly matched his face.

“Dad,” he responded, letting himself be herded by the youngest Sheppard towards the dinning room.

No matter what he and Dave had said at the airport, however, the past hung between them like an axe. His relationship with his father had soured pretty quickly after his mom died, and Patrick hadn’t had any idea what to do with his quietly rebellious first born. So he had spent much of his middle and high school years at boarding school.

His insistence that he would neither get his MBA nor go into the family business the way his dad wanted had resulted in the millionaire industrialist refusing to pay for college. To which John had responded by joining ROTC and getting a scholarship to cover his math degree. His marriage to Nancy a few years after he graduated had smoothed things out a little. She was a perfect high society wife. Then, a few years after that, they had split. And that was the end of that.

As he ate the perfectly cooked filet, John could still hear the screaming match that had resulted the last time he had been at that table.

“You’re throwing your whole damn life away,” his father had yelled upon learning he did not plan to make it work with Nancy and that he furthermore had no intention of resigning his commission at the first opportunity. “I won’t have it John! And I won’t watch you fuck it all up like this! Get out of here until you come to your damn senses. I didn’t put you through the best schools I could find just for you to be so stupid!”

His own furious response hadn’t been much better, of course. He had grabbed his suitcase with one hand and tossed his wedding band on the floor with the other, shouting the whole time.

“You didn’t put me through college, I did! You may have shoved me off on pricy boarding schools to keep me out of your hair, but I got my degree on my damn own. I’m my own man and I don’t need you or your fucking money!”

When he’d slammed the door behind himself that day, nine years before, he had never imagined it being opened for him again, let alone walking through it willingly. Yet, here he was. The food was as delicious as he remembered, and the company just as sullen and silent.

Aside from the occasional forced conversation, it was silent until after dessert had been served, at which point the eldest Sheppard spoke up.

“You hoped some day I could be proud of you? That I could forgive you for not being the son I wanted you to be? Really? That’s what you fucking thought?”

John swallowed the bite of fluffy mousse with a grimace at the sound of his own words. He hadn’t intended to say anything to his father in that message he’d recorded while they were waiting for the Wraith to arrive. But he’d thought he was going to die and hadn’t bothered to tell Chuck to edit it out.

“I don’t know,” he admitted roughly when it was clear that no one else was going to say anything. “It was a bad time, okay, we thought…” He waved off the rest of what he was going to say. There really wasn’t any way he could explain his circumstances when the video had been made. “I’m sorry. I didn’t take the time to actually think about what I was going to say and then it just came out, and… It was a bad time, okay?”

He could see his father’s knuckles turn white where he was gripping his spoon. Dave was sitting so perfectly still he actually watched for a moment to make sure the younger man was still breathing.

“How bad?” the businessman asked, causing his eldest to pause. That was not what he had expected to hear. But there was only one answer he could honestly give.

“Bad.”

The three men finished their dessert without another word. When it was time to leave the table, Patrick spoke again.

“I tried to find you. After we got the video. But no one would tell me anything about your posting other than that you were unavailable. Even my business contacts at the DOD couldn’t find anything.” The older man rubbed his hand on the back of his neck.

“I wanted to yell at you about it. The video, the silence beforehand, and after. I hate what you do for a living,” Patrick ignored the way his son clenched his teeth. “But I don’t hate you. I know you’re a damn fine soldier. I know you’ve become a strong man and a capable officer. I’ve talked to quite a few people about you, John. I know some of what you’ve accomplished. And I am proud of that. And don’t you ever fucking think otherwise, you hear me?”

Lt. Colonel John Sheppard swallowed his shock, and a few other emotions he wouldn’t name. He just nodded to acknowledge his father’s words. Patrick nodded back and waved a hand between the two brothers.

“Dave, show him the room Reena made up for him. I’ve got a conference call with Beijing in ten minutes.”

They watched their father stomp off to his home office without another word and just made their way up the stairs to the largest guest room. Eventually they even had a halfway decent conversation before the younger man wandered off to bed a few hours later. John didn’t expect to sleep well, but before he knew it morning had come and he was alone in the house with his father. The older man had apparently been forced to take a few days off by his ‘overly dramatic doctor’ and Dave was handling the day to day for him at the office.

He came down the stairs braced for the worst, assuming without his brother there to provide a buffer that he and his father would devolve into a shouting match by noon. It was surprising, therefore, when Dave wandered in for dinner that night and he realized the whole day had passed without any major fights.

The tense but hopeful mood was ruined the moment the youngest man opened his mouth. “John. I got a message today you need to see.”

The officer narrowed his eyes but took the slip of paper anyway. As soon as he read it, the color drained from his face and he pinned his brother with a hard look. “Is this some kind of joke?”

“Christ, John. No. Of course not. I verified her identity and even called Bethesda. They have a patient named Anthony DiNozzo Jr. And he did, in fact, have the Pneumonic Plague.”

“The what?” shouted Patrick.

“He’s an NCIS agent, whatever that is. Apparently it was a work thing because when I called his office they told me they couldn’t discuss the investigation and were not able to disclose Agent DiNozzo’s status to anyone but his emergency contact or family.”

“Naval Criminal Investigative Service,” John automatically explained, even as his thoughts spun in an entirely different direction, “He’s been there a few years.”

He hadn’t talked to Tony since before he was stationed at McMurdo, but other than Rodney, he considered Tony his best friend, and had since they met in boarding school when he was fifteen and Tony was thirteen. “The fucking plague? Seriously?”

Dave nodded, then glanced over to their fathler, who was on the phone a few feet away arranging for the family plane to be fueled up and a flight plan filed for D.C. John shook his head, rubbing a hand over his face as his father corralled him into a car and off to the airport.

“The fucking plague,” he said again under his breath. He heard his father and brother both make equally incredulous noises.

“I didn’t know you two were still in touch,” Patrick eventually said, breaking the silence as they sped down the highway.

“It’s been a while since we talked, but we’re still friends.” Green eyes finally started to clear for the first time since he’d read the message. “Why the hell did Senior’s secretary call dad’s office?”

Dave scowled. “Apparently he’s busy with meetings and couldn’t get away so he was passing the message along to you.”

The muttered argument that resulted from that statement kept them all busy badmouthing Anthony Senior in a way that made John think of summers at home when he was sixteen, before he started applying to colleges. Before he knew it, he was boarding the small plane for the second time in two days and promising to let Tony know that Patrick would arrange for a specialist if he needed a better doctor.

“And don’t forget to stay in touch this time, Jonathon, I don’t care where you’re stationed. Understood?”

John accepted the pair of rough hugs and the unexpected parting words from his father. Then he buckled in to fly to DC. To see his childhood friend who had only just survived the plague. And he thought life on Atlantis was weird.

– – – – –

Tony blinked. The light in the room wasn’t blue anymore, but the glare coming from the bright white florescents actually seemed to lend an extra surreal quality to what he was seeing. There was a dark haired man seated in the hard plastic chair only a few feet away from his hospital bed.

An Air Force Lt. Colonel, based on the insignia on the BDUs. It took several seconds for his brain to process the sight. “John?”

The other man looked up at the incredulous sound. A smile, wilted though it was, spread across the officer’s face. “Hey buddy, finally awake I see.”

Tony just blinked a few more times. The phrase ‘what the hell’ rattled around in his head but when he tried to voice it, he only managed a weak cough. And boy did that not feel good. But it was certainly nice when his old friend responded without even needing to hear a question. They may not have spoken since the man’s last tour in Afghanistan, but obviously the three years of silence hadn’t done too much damage to the friendship they had first formed in boarding school.

“They haven’t given you any of the good stuff, buddy. You need something for the pain? Or are you high enough on my amazing yet unexpected presence?”

The agent did his best to smirk even as he shook his head, the movement slow and careful. “None of the good stuff. You know it makes me stupid.”

The two exchanged a very telling look. John had been there, after all, the summer before Tony had turned fifteen, when the younger boy had broken his arm – ostensibly playing basketball with his father – and been sent back home with very effective pain medication.

For someone who barely spoke to anyone other than John and the DiNozzo cook, he had spent at least an hour rambling about anything and everything. Including the fact that while his father had been on the small court in their backyard with him when he was injured, father and son had not been shooting hoops together in some form of family bonding exercise as Senior had told the ER doctors.

“Well, we wouldn’t want you to embarrass yourself in front of all the pretty nurses, now would we?”

Tony tried to smile at the old joke. It had started their last year together at boarding school when they had spent a very long few nights in the school infirmary with a bad case of the flu. Tony had almost been sent home, but by the time Senior had gotten around to returning the school’s call, he was already improving. By that point Patrick had made a quick visit to check on John and both boys had driven the two nurses on site a little crazy. It was the first time the shy Tony had ever tried to flirt with a girl and it had been the only source of amusement either had.

Tony assumed the other man could see he wasn’t quite up to joking around yet, as the soldier decided to address the question they both knew Tony had and just hadn’t felt up to asking.

“So, not exactly who you expected to see, huh?”

If the slightly younger man had been feeling better, the glare he sent John’s way probably would have been painful. But Sheppard just smiled and waited a full five seconds before he went on, probably just to watch his friend try to glare again. He would have complained but it felt good to mess around like this with John, the way they used to. Besides, he would recover soon enough and then he could return the favor.

All thoughts of future pranks disappeared when he finally got the answer he was waiting for. It was the absolute last answer he ever expected to hear. “Turns out there was some contact info for your old man somewhere in your files and he was called last week.”

They both pretended Tony’s wince was a result of his less than comfortable physical condition and not caused by the mention of his father being told he was dying of plague. Especially given the obvious lack of Senior’s presence at his son’s bedside.

Once the worst of the shock wore off, the agent narrowed his eyes and tried to wordlessly demand the rest of the explanation. Because someone calling Senior did not explain why John was there. It either worked, or the other man decided to continue on his own.

“Well, it would seem that Mr. DiNozzo was in the middle of a business deal and didn’t have the time to respond to the message the hospital left with his admin. So he had his assistant pass it along to someone who might be able to do something about it.”

Tony did his best to breathe past the pain in his chest, silently insisting that he just needed to go through a couple of the breathing exercises Brad had tried to show him. Because the pain he was feeling was just another lingering symptom and had nothing to do with what John was saying in that vaguely familiar flat tone he used to use when discussing his own father. That insistence was a little more difficult to maintain, however, when his old friend finished his explanation in an even more stoic tone of voice.

“Apparently he wasn’t aware that we hadn’t been in touch lately, and just assumed that we were still close enough that a request to check in with you would be easy for me to fulfill if passed on. Through my father.”

“Shit,” the younger man muttered, the word coming across clearly despite the rasp of his lingering cough. Senior obviously hadn’t kept in touch with Patrick Sheppard if he didn’t know the successful businessman hadn’t spoken to his elder son in almost a decade. Of course, the fact that Patrick was in fact a very successful businessman probably explained that. For all Senior’s pretentions, his company was nowhere near Sheppard Industries and hadn’t been for decades, if ever. “Then how…?”

The head of messy black hair tilted slightly in recognition of the partially formed question. “Some stuff happened at work a while back and I made some inroads to opening things back up with Dave and the old man.”

Green eyes narrowed and watched the Air Force officer rub a hand on the back of his neck for a moment. Neither said anything. Knowing as little as he did about the other man’s career, Tony knew better than to ask what ‘stuff’ at work would have prompted such a thing. Before the silence dragged on too long, John continued his explanation.

“I happened to be… around, this week, and figured I might as well call the office. See if we might talk, or whatever, while I was here. So we did. Talk. A bit. Had dinner, spent the night.” The two exchanged incredulous looks. Well, Tony’s was probably supposed to be incredulous but he figured it ended up looking rather pained. Then John went on.

“Even hung out with the old man most of the day, and boy was that weird. My dad was out of the office so Dave was filling in on a few things. Including fielding less urgent phone calls and stuff. He got the message from Senior’s assistant yesterday, so he passed it on to me. After making sure it was real, because, well, plague.”

John was the only one with a shocked expression that time. Tony just tried to shrug his shoulders. It must have worked because the dark-haired man raised a single brow, then shook his head. “Anyway, Patrick called up the family plane. Then offered you a super expensive specialist if you don’t like the docs here, by the way. And here I am.”

John spread his hands a little as if to say, ‘there ya go.’ Tony just blinked a few times in silence, mentally reviewing what for his occasionally taciturn friend, was practically a lengthy monologue. There were more than a couple things that he wanted to question. But he just didn’t have the energy to have a serious discussion at the moment. So after a few breaths, he just nodded and gave as much of a smile as he could manage.

“Good to see you, man.”

John nodded back, acknowledging the words he hadn’t said as much as the ones he had. “Sorry it took so long, Tony.”

The agent managed a short headshake. He’d heard about what happened in Afghanistan. He hadn’t been at NCIS for long at the time, but it had been long enough to have developed a contact or two. He probably knew more than John would have been comfortable with regarding what had occurred and why the pilot had been shipped to freaking McMurdo with a black mark on his record.

In what was probably an attempt to distract and lighten up what Tony was sure was a miserable expression on his face, his oldest friend briefly squeezed his hand, then leaned back in the uncomfortable chair. “So, I’ve been stationed on the ass end of nowhere for almost two years. What movies have I missed?”

Tony smiled much more convincingly that time, took as deep a breath as he could without coughing, and dove right in.

Chapter Three

His gaze flicked back and forth between Caldwell, McKay, and the screen of the tablet he had been handed as soon as he entered the conference room. Setting the device on the table, he rubbed the back of his neck and tried to hide his frustration. John hadn’t even had time to unpack the small bag he had brought with him to Earth, let alone settle back in on the city, and already he was being confronted with all the loose threads that had been dangling – and in fact unraveling – during his time in the Milky Way. As completely unrealistic as it was, a very small part of him had hoped that by the time he got back, some of Weir’s mess would have been dealt with.

Instead, the mess just kept getting bigger. Or, more to the point, the fact that there had been such a huge mess hiding in the background just kept getting more apparent. He gave in to the urge to sigh but bit back the desire to ask how things had gotten so messed up without them being aware of it.

“We’re going to have to have some kind of full scale inquiry,” John was rather relieved to note that there was no trace of a whine in his voice, despite his overwhelming desire to do so.

“I think we can all say that the situation here is much larger than just the matter of Dr. Weir having hidden an obsession with ascension,” Caldwell responded in a flat tone.

Rodney made a rude noise in the back of his throat, but any response was cut off by a request over the radio that called for the attention of the new official expedition leader. McKay and Sheppard watched the Colonel leave the room with a sharp nod, the younger soldier waiting for the door to close behind his superior officer before deflating in his seat.

“Fuck,” he muttered, as both hands rose to cover his face. “How did we not see any of this?”

The newly reinstated CSO tossed his tablet onto the table with far less care than he would normally show his computer. “Hell if I know. I mean, she had Ford’s promotion paperwork all filled out, Sheppard. Ford. As military commander. What the hell was she thinking? How did we not know she was bat shit insane?”

“You don’t have to point out to me how bad of a strategic decision it would be to place a green Lieutenant in charge of a force of one hundred and five marines in the middle of a war zone, McKay,” bit out the career soldier.

The scientist shot the taller man an almost repentant look. “Right. Sorry. I just… John, I don’t understand.”

Sheppard couldn’t help but think that a lot of people would assume that the cost of admitting his confusion would be far too high for Rodney to bear. But he knew that his friend was well aware of his lack of social finesse and found it completely excusable. McKay didn’t care that much that he missed the nuance of human behavior and motivation, such things were hardly real science, after all. But in this instance, they both knew that their having misjudged Weir’s behavior and motivations was coming back to bite them all.

“Was she preparing some kind of back up plan? Was replacing you some kind of long-term goal? I mean, I know she was more interested in talking to Ford than me when we were stuck in the jumper that time with the bug and all. And obviously he wasn’t going to know the first thing about what was going on with the ship or the ‘Gate. But I just figured she didn’t want to talk to me because she didn’t want everyone to see how little she understood about the jumper or the ‘Gate.”

John let himself chuckle just a little at the frustrated ramble, even if the sound was more tired than amused. He was silent for several moments. “Do we know how old the file was?”

“It was created after the nanite bio-weapon got loose. And it was updated after the whole retrovirus blue bug thing.”

The corner of his lips quirked outward just a little. “Yeah, I can see that. Elizabeth was quite put out with me for not staying out of that situation. And she was definitely not terribly happy with having Caldwell in my place.”

Blue eyes narrowed, most likely at the barely-there smirk that he could feel lingering on his face. Rodney didn’t have the time to prod the reasoning behind it before he continued.

“But as for what she was thinking? I really don’t think we will ever actually be able to understand that, because you are right. The woman was bat shit and unfortunately for the rest of us, very good at hiding her crazy.”

“Right?” the CSO agreed with near outrage. “As much as I hate having to give up spots for real scientists on the roster, I did agree that the psychologists were here for a reason. What the hell have they been doing, anyway? This is the kind of stuff they’re actually good for. I might have wasted some of my time checking on this kind of thing if I thought they were all falling down on the damn job.”

John had a sudden image in his head of the snarky, impatient McKay wandering around the city with a clipboard and demanding that each expedition member declare themselves sane enough to be there. He would give each one an incredulous look, demean their intelligence, then check them off, and move on to the next.

The soldier couldn’t help but laugh at the thought. The way his friend immediately gave him a suspicious look very close to what he had pictured only made him laugh harder. After several moments, the military commander gained control of his amusement and managed to wave off the unasked question he could see being directed at him.

“Sorry,” he got out between the fading laughter. “Maybe we should arrange some city-wide welfare checks of some kind. There really should be yearly mental fitness evaluations for the civilians like the ones the military regs demand. They may not be considered field assets or be technically required to maintain those types of standards, but a war zone is still a war zone.”

Sheppard ignored the disgusted expression the scientist made at the thought of mandatory psych evals beyond what he had to submit to in order to remain qualified to be on a ‘Gate team. One hand ran through his messy black locks as his own expression grew serious. “Field readiness in general should be a consideration for civilians out here. Just because they don’t leave the city doesn’t mean they don’t need to be able to defend themselves in those types of situations. Or at least not be a liability to the rest of us.”

McKay’s face twisted again. It wasn’t the first time a similar idea had been mentioned, but no doubt the thought of losing some of the almost capable scientists he had because they couldn’t hold a gun was no more welcome than it had been before. He cleared his throat roughly with yet another grimace as he reluctantly admitted they might need to talk about such a thing at their next meeting with Caldwell.

“But not now,” Rodney half demanded, half pleaded, as he pushed himself to his feet to top off his coffee. “Can’t you be on the city more than thirty minutes before you add yet another thing to our list of messes to deal with?”

Both eyebrows rose at the almost antagonistic tone suddenly being aimed at him. He started to respond, to remind the CSO that he had been summoned to the meeting before he even got unpacked. Then McKay dropped gracelessly back into his chair and took a long drink of his caffeine.

“Fuck. Sorry.”

Green eyes narrowed as they took in the exhaustion that was suddenly clear in the other man’s face and body. As tense as his meetings had been on Earth and as stressful as the trickle of information had been regarding the city had felt for him on the Daedalus, he hadn’t been in the thick of things getting that information.

Rodney, on the other hand had been shunted unwillingly into an administrative position he didn’t want and forced to spend two months dealing with the fallout first hand, as well as sharing the leadership burden with a career officer he barely knew. And John would bet anything that the astrophysicist had been unable to stay out of the day to day running of the sciences despite Radek’s temporary promotion.

“You okay, there, buddy?” he finally asked, only somewhat jokingly, shifting closer, until the arms of their chairs practically touched.

He squeezed his friend’s shoulder. Noticing how tense the muscle was under his hand, dug his fingers in, briefly massaging Rodney’s shoulder and the base of his neck. The lighthearted tone pulled a weak glare from the other man that none the less cut the tension that had started to grow in the room after Rodney’s uncharacteristic apology. They stayed like that for a couple minutes, the CSO slowly letting his head fall onto John’s shoulder to rest for several long seconds before he sat up and the soldier let his hand drop back onto the armrest of his chair.

“Next time everything goes to hell you get to be in charge of all the stupid people,” Rodney demanded with a slight pout.

“Deal,” John acquiesced gracefully. He reached out again and grasped the scientist’s free hand, squeezing it for a couple of seconds in reassurance. “In the meantime, why don’t we both get some downtime in before Caldwell finishes whatever he had to do and calls another meeting?”

McKay rolled his eyes but began gathering his tablets to leave the room, grumbling all the way to his quarters. He was still grumbling more than a week later when they left yet another meeting. Juggling the various angles of the investigation into the effects Weir’s actions had had on the expedition along with the day to day running of the city was stretching things out far more than any of the senior staff was comfortable with. John knew from his latest rant that Rodney was still not caught up with reports and projects in the various sciences from his stint as co-administrator.

If nothing else, the extra complications from Weir’s abandonment of Atlantis had given his friend plenty to complain about. Sheppard himself was enjoying the grumbles and hand gestures as the scientist regaled him with tales of his minion’s inability to follow the new lab standards he was implementing. The interruption on his entertainment left the soldier frowning when Rodney suddenly froze in the middle of the hallway.

“Oh. Before I forget. You had an email come in the last databurst. It was from somebody named Tony and well… I mean, I didn’t read it or anything, but I saw the subject line and well… you probably want to read it.”

John’s brows furrowed in concern and he grabbed one of the spare tablets that his friend always carried around. Starting back down the hall, he began logging into his personal email, completely ignoring the indignant exclamation his actions spurred from Rodney. The offended noise cut off when they reached his quarters and the soldier sat heavily on his bed as soon as he was logged in.

“So, uh. Who exactly is Tony? I don’t think you’ve mentioned him before.”

Sheppard blinked at the screen in silence for a full minute, unable to look away from the words in the subject line. It simply said, Kate is dead. He took a deep breath, then looked up at the scientist as if finally registering that he had been asked a question. “What? Tony? We met when we were kids. We were good friends. Are good friends. We didn’t talk much after I was transferred to McMurdo, but I saw him while I was on Earth. He, well, it’s a long story. We’re back in touch and… shit.”

He could feel himself being watched as he logged out and handed back the tablet, but Rodney stayed uncharacteristically silent while he gathered himself. “Tony’s a cop, well technically he’s a federal agent. He works for the Naval Criminal Investigative Service and ended up in the hospital. I got word shortly after my debrief and we hung out most of the time I was on leave. He’s on a four man team. Kate was his partner.”

Silence descended between them once more and the astrophysicist’s mouth opened, then closed twice before he finally blurted out a single word. “Beer?”

The look of relief on Sheppard’s face was soon mirrored on Rodney’s when he answered. “Fuck yes. I brought a few movies back with me.”

It took a moment for McKay to response to the non sequitur. “I’ll get the beers if you set up the movie?”

Rodney looked inordinately accomplished when John responded with a wide smile and they quickly went about seeing to their assigned tasks. That they managed to get through the entire six pack and the whole film without being interrupted for an emergency somewhere on the city was almost as satisfying to John as the chance to wind down with his best friend. Even if worry for his childhood friend lingered in the background.

– – – – –

Tony woke from a dead sleep, already wiping frantically at his face, trying to clean off blood that wasn’t there anymore and hadn’t been for a week. Kate’s blood. Kate was dead. The statement had run through his head so many times, the event played out so frequently in his mind’s eye, that he couldn’t take a single breath without the reality washing nauseatingly through him. Awake or asleep.

Not that there had been much sleeping. Even taking into account that he hadn’t healed a hundred percent from his brush with the plague – he was frankly a little surprised he had been cleared for field work already – he had barely slept. How could he sleep when he could be hunting Ari instead?

How could he sleep when he just ended up seeing Kate smile, then freeze, then fall, a bloody hole dead center of her forehead?

He levered himself out of bed with a heavy sigh, making his way into his kitchen and opening his freezer to see if anything good remained from what John had left behind. Just before he left town a month before, Sheppard had insisted on stocking him up with what he called ‘pampered MREs.’ He would have argued with his friend, but as much as he liked to cook, he hadn’t felt up to doing more than heating a frozen TV dinner, so he’d allowed the other man to fill his freezer with a wide selection of them.

He was grateful now to have the dozen or so that were left. They were quick and hot and despite their otherwise small size, they were enough to fill him up. For all that he normally ate more, between the extended course of antibiotics – a stupid precaution after antibiotic resistant plague, in his opinion – and the pain killers he had recently finished with, it was about all his stomach was able to handle.

It was also all he had time for, as no sooner had he tossed the cardboard plate in the trash than his phone had chimed with a text from the office. One of the many searches he had left running had finally come back with something and he needed to join McGee in the field to track down the meager lead. Any trail was worth following, he admitted as he grabbed his coat and locked the door behind him.

It was several trails and a bleeding heart Mossad handler – and what kind of contradiction in terms was that – that finally led them in the right direction. Hours of running on fumes and rubbing at his chest as unobtrusively as possible, passed before it all came to a head. Then Ari Haswari was dead.

And Tony DiNozzo was dead to the world, lost in the first full night’s sleep he’d had in far too long. If the lingering image of Kate’s dead body formed a red mist before his eyes for a few minutes after he woke, no one had to know. He certainly wouldn’t be mentioning it in his next email to John.

– – – – –

A little over two weeks after the city’s military commander had returned, its CSO found himself scowling as he made his way through the corridors to John’s door. Green eyes rose from where the soldier was tying his boots, surprise and a hint of suspicion in his gaze as Rodney stomped into the room.

“How long exactly have you been a trouble magnet and how far does your reach go? Seriously.”

One brow rose in question but the scientist waved dismissively and grabbed his friend’s tablet off his otherwise unused desk. Sheppard caught the computer with a glare, but didn’t interrupt when McKay continued.

“Check your email. And for the sake of Miko’s minions’ questionable stability, tell your friend to stop putting the word dead in his subject lines, it’s scarring the stupid ones.”

Rodney rolled his eyes again, watching John scramble to access and read his latest email from Tony. ‘Ari is dead.’ Honestly, he thought to himself, what kind of person just keeps doing that? At least the one about his partner had content. From what he could tell, this one didn’t say a single word in the body of the email. Though there was another message from the same sender in the databurst, so maybe it gave some context.

The scientist paced around his friend’s room for several minutes while he went through his emails, not wanting to admit how curious he was about what was going on. He certainly wasn’t concerned. After all, it didn’t effect him in the least what kind of drama this other person had going on. It did effect John, though, he admitted as he watched various emotions flit over the soldier’s face. And John was his friend. So, in a way it effected him too. Damn, he cursed silently. He was going to have to get involved, wasn’t he?

McKay scowled, even as he mentally composed an email of his own to send. He was interrupted briefly when Sheppard muttered out a brief, incomplete, explanation about the investigation into Kate’s murder as they made their way to the mess hall. But Rodney was a genius, after all, and had no trouble simultaneously listening and mentally composing an appropriate warning. He was quite happy with his efforts when he finally got around to typing them out and sending them with the next databurst.

The scientist was less happy – though reluctantly amused – by the response that warning received the next week. McKay scowled at the screen, absolutely not suppressing a laugh, as he scrolled through his to-do lists for the day. He didn’t quite get half way through before he found himself snarking out a reply and setting it to transmit with the next burst.

– – – – –

Tony stared at the screen, fingers poised over the keys as he tried to think of what to say. It had been almost a week since he had sent John an email and he knew he had to tell his friend something other than Ari is dead. If he didn’t say something today, he was sure to have a very strongly worded reply to those three words the next week.

One thing he had to say about whatever backwater base John was stationed, the limitations of their outside communications meant that his email exchange with the other man was exceedingly timely. Even with his crazy schedule, Tony was able to say something in time for the once a week data package that was sent and received by the base. The electronic back and forth had become almost a touchstone for him since he had gotten released from the hospital.

And yet, it took almost twenty minutes for him to type out a coherent explanation of the terrorist’s demise in Gibbs’ basement. The fact that the event didn’t quite make sense to him probably came across more clearly than he had intended, but he hit send before he could convince himself to sensor his words.

Quickly shutting the computer and grabbing his keys, Tony left his apartment and made his way to his car, then to the Navy Yard. For all that he was sure the official sequence of events didn’t line up, he had no intention of telling John what he thought really happened. His friend had his own problems based on the brevity of his last few emails. Neither one of them seemed able to go more than a line or two without their professional tension leaking into their words. Thankfully, they both appeared to have made an unspoken agreement not to point out each other’s issues unless something forced the issue.

Kyle Boone and his crazy murdering lawyer didn’t force the issue. But it did make him wish he had stayed home that day. By the time he flopped onto his couch, he was more exhausted than he had been since the lingering effects of the plague had begun to fade. He had barely enough energy to reach out and open his computer, resting it on his chest as he opened his email. The position was awkward and left his neck bent at too sharp an angle, but he just couldn’t force himself to sit up.

He was still sprawled across his couch when he finally got the first of the three new emails from John opened up. He clicked on one with his eyes half closed so didn’t notice that the message wasn’t actually from his old friend. As soon as he started actually reading the contents, he sat up abruptly in surprise, having to grab the laptop to keep it from falling to the ground at his abrupt movement.

Repositioning himself and the computer, he read the rambling paragraph of insults more carefully. The main portion of the email contained a rude demand that he better have the limited intelligence remaining after a career idiotically chasing a leather ball that your current employment almost indicates and be smart enough not to mess with John, or the IRS will be even more interested in where your trust fund disappears to than you will.

When the shock of the words and the unfamiliar signature line had worn off, Tony had found himself re-reading the wordiest ‘shovel talk’ he’d even heard. Then he’d laughed until he’d had both hands pressed to his chest in an effort to counteract the ache.

Whatever language had littered the rest of the short and insulting email from Dr. Rodney McKay, PhD., PhD., the proof that his friend had someone on his six who was looking out for him on missions and on base, was far more of a relief than he had thought possible. He may have spent a number of years without any kind of contact with his friend, but he certainly had no intention of allowing this chance at reconnecting to slip him by.

He hadn’t realized how much he missed John until he’d woken in that hospital room to find his friend sitting next to his bed. He hadn’t quite realized how much he had been pissed off by being told that Ziva David had been assigned to his team, until he opened his computer to respond to another email from John.

He had stumbled into his apartment that night without clearly seeing anything. He wasn’t sure, at all, how he had gotten home. He just kept seeing the bullpen with her there. As if she had a right to be inside the building, let alone at Kate’s desk.

Tony made his way over and dropped onto the couch. When he noticed that his computer was not on the coffee table like it usually was, he looked around his kitchen and living room as if he didn’t even recognize it. His eyes finally fell on the laptop, sitting innocently on the breakfast bar where he had left it that morning. It was a long moment before he levered himself to his feet and suddenly found himself staring at the sleeping screen.

Opening his email program was done without any thought at all, and before he was even aware of having done so, he was looking at a blank email. His fingers paused over the keys while he thought of what to say. The day washed through him, painful and sharp and left him spewing rage and pain and frustration into a message to Lt. Col. John Sheppard of the United States Air Force.

Once he started typing, he couldn’t stop. It started to pour out of him. How he had walked into the bullpen that Monday morning and found Ziva David of all people sitting in Kate’s chair. How he had been told that the director had assigned her to his team. How Gibbs had decided that was completely okay with him.

Tony stood after a few minutes, unable to sit still even to type, and began to pace back and forth. How on earth did Gibbs not see that putting Ziva in Kate’s place was an absolutely horrible idea in every possible way? How did he think it was okay when having the foreign operative on the Major Case Response Team was so far out of line that the distance couldn’t even be measured?

How, he asked himself as he ran a shaking hand over his face, did his boss not care enough about his living team members to fight this? How did Gibbs – sempier fi, always a Marine, never leave a man behind, never betray your partner – have so little respect for Kate that he would replace her with someone complicit in her murder? The confusion, the hurt, drained enough of his restless energy that Tony was able to retake his seat in front of his computer and continue to vent to the only person who would listen.

She was his handler, John! Her entire job was keeping track of everything he did and coordinating his actions. Getting him the information he needed to do all the things he did. Including dossiers on the people he would deal with. And considering how much she knew about Gibbs and the rest of us, there is no way she didn’t have tons of info on us for Ari. And herself.

She fucking profiled us for him. And she acted all innocent and like she thought there was no way he could have killed Kate. Either she wasn’t doing her job at all or she was lying through her teeth, pretending to have perfect faith in her beloved brother. So she’s inept or a trained actor who tried to play us all. I don’t see how she could possibly be appropriate to be on the MCRT. Not to mention she’s fucking Mossad! Mossad, John. A fully trained Kedon fucking assassin who has never investigated a crime and can’t legally sign for or handle evidence. Not to mention an abrasive bitch who would surely be the biggest disaster ever if she tried to testify in court for a case.

This is who is sitting in Kate’s chair. With her smug little smile and not a single concern with how that chair became empty for her to sit in. Like her precious brother didn’t blow off my partner’s head feet away from me only nineteen days ago. She’s on my six in the field. And Gibbs thinks it’s no big deal. Thinks everything is fine and the rest of us should be fine with operating under whatever rules he makes up for his team. Not our team. His team. That now has an official Mossad Liaison Officer.

What the FUCK?

He sent the message without an ounce of concern that he had just vented his spleen through a communications system that was possibly as well monitored as access to MTAC. Then he poured himself a couple ounces of really good scotch and didn’t have a single concern about anything for a full hour. After which he realized he had told the military commander of a classified base that he now had a foreign intelligence operative on his investigative team. Through an email system that would be read by who knows how many other military personal with clearances higher than his.

Tony set the now empty glass on the table. Then reopened his email and slowly worked his way through an apology.

Shit. Sorry man. Didn’t mean to spew all over you and whoever has to screen your mail. There’s got to be some weird ass intergovernmental kiss ass thing going on that I totally don’t know about where NCIS and Mossad are winning stupid love-your-neighbor, bipartisan, international cooperation PR political brownie points for whatever the hell this is. And we all know political maneuvering makes fuck all sense. Right?

I’m being overly emotional because I had my partner’s blood spray all the fuck over my face and can’t work through my own shit to see the upside to having the daughter of the head of Mossad on my team. So, it’s all fine and I will do as I’m told and catch killers and solve crimes and learn what I am sure will be many interesting curse words in Hebrew. Should be fun. And yes, John, I am completely drunk right now. Aren’t I articulate when I’m intoxicated? I guess I learned something from my father after all.

He hit send and let his head fall back onto the couch. It took another glass of scotch before he could get to sleep, and even then, his rash words and the insanity that had spawned them chased him into his dreams.

– – – – –

When John had sat down at his desk that bright Friday morning in early October, he had been anything but enthused about diving back into what he could loosely term their investigation into the mess Elizabeth Weir had left behind her on Atlantis. So he logged into his personal email instead of the files he should review before the upcoming meeting with Rodney, Miko, and Caldwell.

The first thing he saw were two emails from Tony from that morning’s databurst and he happily clicked the first. Well, the first on the list, not the first he had written. Which meant he was very quickly pissed and confused and rushing to open the previous email so he could figure out what the fuck his friend was talking about. Then he was just really pissed. And still a bit confused. After a few loud curses, he went back and re-read them both, this time in the proper order.

Having finished reading, the military commander of Atlantis simply stared. After several moments he couldn’t help but echo the end of his friend’s first message. “What the fuck?”

The shock quickly faded and anger rushed back in to fill the void. He let some of that anger out as he banged at the keyboard, typing up a quick reply.

Fuck that. You were right the first time. That is messed up. And don’t let that bitter old jarhead make you think you’re the one with the problem here. You are being anything but overly emotional. And as much as I agree about this SNAFU probably being some incomprehensible political maneuver, that doesn’t mean it’s right. Or that it’s not completely understandable for you to have a problem with it.

Any red-blooded human being would have a problem with that. The only ones who are messed up in the head are Gibbs and your director for thinking your team was the place to shove their little political brownie points.

As for your email causing either of us any problems, don’t worry about it, buddy. Rodney has an algorithm that goes through things on this end, and Carter takes care of things on the other end. If anything gets triggered, I’ll just send her a few lines to help explain the context. And that should be that. After all it’s not like you said anything that isn’t official record anyway.

And yes, Tony you are very articulate when you drink. I hardly think Senior deserves any credit though, despite his shinning example of how not to act when intoxicated. You raised yourself damn well, buddy, and don’t let anyone tell you different. Unless it has to do with your singing voice. Steve is an idiot, because that still sucks.

John grimaced at the half-assed attempt at levity with which he had ended the message, but having no idea what else to say, hit send and leaned back in his chair with a muttered curse. He absently reached for his coffee with one hand and ran the other over his face while he continued to silently degrade the various levels of command at NCIS. Shaking his head, he struggled to mentally grasp what the hell was going on in D.C.

He spent most days dealing with crazy alien messes and space vampires so his scale of fucked up was not average by any means. Yet even he considered a foreign intelligence operative and trained assassin assigned to an investigative team at an organization that had access to classified and confidential data to be fucked up.

That was without taking into account the fact that said operative had played at least a peripheral role in the murder of a former member of that same team. And from what he had read between the lines of Tony’s email the week before, probably had some involvement in the death of her asset who had committed the murder.

“What the fuck?” he said yet again to the empty room. Well, not completely empty as Rodney came through the door at that moment, pausing slightly on his way to the carafe of coffee.

“That’s what I was going to say!” the scientist yelled as he filled his ever-present coffee mug. “Have you read your email yet? Because my algorithm showed some very shitty results from the databurst!”

The Colonel wasn’t quite up to formulating a response and so nodded, then gestured at the screen of his computer, which still displayed the email chain between himself and Tony. In the silence that followed, Rodney helped himself to more coffee and glared. Then he made his way behind the desk, leaning over John’s shoulder so he was close enough to read the screen. After a moment, he set his coffee down, braced both hands on the desk and leaned in even closer.

The scientist remained in that position, leaning over his friend closely enough for each breath to cause his chest to brush against the back of John’s shoulder as he read. Finally he stood back up and shot the soldier a disgruntled expression. “Seriously. What the fuck, Sheppard?”

For the second time that morning, the curse startled someone mid-step as they entered the office. Well, two someones, as it appeared that Miko Kusanagi had met up with Caldwell on her way there. The Colonel regarded his military commander and chief scientist with a grim expression. “Is there something we need to address before the meeting, gentlemen?”

John shook his head and tried to wrestle his thoughts back to the agenda they had agreed on the night before, forcing himself to ignore his disappointment when Rodney made his way back around the desk and sat down. McKay didn’t seem to even attempt to work past the appalled anger he was still feeling.

“No, no, just your country exhibiting its political and legal stupidity yet again. Nothing to do with Atlantis this time, though. Just run of the mill idiots in charge of…”

“Pardon?” cut in the stern voice they were both starting to become familiar with.

John sighed and made himself close his email and open the relevant documents he had been compiling for the meeting. “Nothing, sir. I received some less than pleasant emails with the last databurst but they are from a personal friend and have no bearing on the city.”

Rodney scowled at being cut off and consoled himself with a long swallow of coffee as the two military men, and Miko, got themselves settled and began the meeting. By the time they had decided where to begin for the day, the scientist had a fresh cup of coffee and his own share of upsetting reports to discuss. Atlantis had enough problems of its own that were more than adequate to keep them occupied for the time being.

John was sure his friend would pester him for more details later. And probably Tony too. No need to restrict his supply of insults and complaints about NCIS just because he didn’t have the full list of stupid that was going on over there. Though Sheppard was positive that if he wanted a complete list Rodney would just get it himself. He no doubt had a few contacts from before he began working for the SGC that could get that for him.

He was briefly tempted to tell his friend that if certain of those contacts were made aware of the scope of stupidity being exhibited by NCIS, they may well take some initiative of their own. He could even picture the smile that would form on Rodney’s face at the idea of foiling inane governmental dumbasses using their own bureaucracy. Mentally telling himself to forget even the idea of such a thing, he gave his full attention to cleaning up the ridiculous mess Weir had left all over his city.

– – – – –

Terrance had been an agent with the Air Force Office of Special Investigations for almost six years when he had been read into the Stargate Program to assist the SGC with the investigation into the thefts of offworld artifacts and munitions. Because of that, he was one of the only investigative contacts for the classified project.

The initial investigation he had been asked to help with hadn’t actually needed more than a week or two of his attention, solved as it had been with a little undercover work from Jack O’Neill himself and the help of the Tollan. But it wasn’t unheard of for him to receive an email or two a month from someone in the mountain. Hearing directly from Lt. Colonel Samantha Carter, however, wasn’t the norm. So when the email came through that afternoon, Terrance gave it his full attention.

One does not, after all, knowingly owe someone like Carter a favor and not give it their all when that favor was apparently being called in. Which it was, according to the subject line.

Watery brown eyes flicked over the short message and then the file attached. Then they blinked. That had not been when he was expecting. Missing supplies – usually electronics or a personal stash of coffee were actually the most common – and a few files read or a quick trip to the mountain to look through a room and speak to a few people was what he was used to.

A personal email indicating questionable hiring practice at the investigative arm of the Navy came completely out of left field. Terrance blinked some more. Then he re-read everything. Then he sat in silence for several minutes and just thought over the conundrum he faced. There had been no illegal actions taken that he could see, and technically nothing here was within his mandate.

Yet as annoying as it might be to jump through a few hoops to skirt said mandate and obscure where and how he had become aware of the situation, now that he was aware of it he felt unable to just write it off. Besides, he did owe Colonel Carter a favor and if he couldn’t pay her back with this, it would be with something else later. Might as well clean his slate with her by doing something about NCIS, because the woman was right and so was this Agent DiNozzo.

The situation being described in the original emails did not set one’s mind at ease, and all the aspects of the assignment the man complained about were indeed problematic. Not to mention the issues with chain of evidence, evidence processing, interviews, and system access that he could see tripping up a prosecution, and even costing a conviction down the road. The more he thought about it, the more insane it sounded to him.

A foreign intelligence officer had no place conducting the myriad tasks of an investigation that required specialized training and oaths of office she would be inherently unable to complete simply by being Mossad. And that didn’t even take into account how easily a defense attorney could capitalize on such a thing in court. Her mere presence could guarantee that evidence be thrown out and a case lost. Come to think of it, that was probably where he should start. Rubbing his hands together briefly he picked up his office line and dialed his contact at JAG.

“Yes, good afternoon, this is Agent Terrence Sunders from AFOSI. Does the Judge Advocate have any time on his schedule this week that I might meet with him?”

– – – – –

Tony gritted his teeth and kept his eyes resolutely away from the desk he still thought of as Kate’s. Just the sight of Ziva sitting there was hard to take, let alone the disdainful looks shot his way whenever she glanced in his direction. He said nothing about the looks. He said nothing about her comments or her insults or her abuse of the English language. He said nothing to her at all unless a case required it.

He occasionally did his best to goof off and keep the atmosphere in the bullpen light between himself and McGee, but even those attempts at camaraderie were getting fewer and further between. It just wasn’t worth it, he decided as he ignored the way his probie was spilling food all down his shirt in an attempt to eat using the chopsticks that had come with his lunch.

Tony had been hopeful when he’d convinced Gibbs to bring McGee onto the team that he and the tech expert would develop the kind of working relationship that he’d shared with Kate. One part snarky annoyance, one part friendship, two parts professional determination. But the way the younger man had begun laughing at Ziva’s insults and not-so-friendly jabs, and then offering his own? If he wanted camaraderie he just had to wait for the weekly emails from John to come in. And from how often he had been sending them, he should be receiving more than a couple replies this Friday.

He didn’t need to look for that kind of connection at work. Certainly he didn’t need to look here for any kind of support as far as his opinion of their liaison officer. Because he wasn’t going to get it. As Gibbs suddenly swooped past the desks and barked out a demand for them to get their gear, he reminded himself that he wasn’t going to get anything other than a sense of professional accomplishment at a job well done.

A moment later he rubbed the back of his head absently as he rode the elevator down to the parking garage, apparently having earned a head slap for moving too slow. Ziva and Tim exchanged a grin and a smirk that did not go unnoticed by the senior field agent. So much for professionalism.

– – – – –

John startled at the sudden clang of a coffee mug hitting the desk in front of him. The three others in the office jumped slightly as well. The Lt. Col. slumped back down and tried to return to his reports, but the others continued staring and fidgeting until Rodney glared them all down. The sight of his men doing their best to tiptoe around the CSO for nearly a minute before the scientist huffed loudly was more than a little amusing.

“Seriously?” The single word was accompanied by an irritated waving of hands that sent the security team scurrying off for their lunch break.

John’s head dropped onto the back of his chair, rolling slightly as a few chuckles escaped. “Jesus, McKay.”

“What?” demanded the other man, half defensive, half amused.

The officer just laughed harder, tapering off as his friend began to eye him suspiciously over the desk. “Thanks, buddy, I needed that.”

Rodney just continued to stare, eyeing his friend in judgmental silence for three solid beats. Then he waved one hand dismissively and sat forward. “I heard you get called down here over the radio hours ago. How much more trouble are you about to cause?”

John rolled his eyes, leaning forward as well. “Way to blame the victim, Rodney.”

“Oh, please. Like you haven’t had a little hissy every time I have uncovered yet another stupid thing wacko-Weir left for us.”

Sheppard glared. Rodney glared back.

“Anyway,” John dismissed with only slightly less good humor than he would normally use to disregard his friend’s characteristic abrasiveness. “I’m not sure yet how much of this particular mess is a direct result of the crazy. I think a lot of it is just lack of training and things falling through cracks. Though admittedly a lot of the cracks are probably a result of the crazy. And some of the reason for lack of training. Or at least what ended up being a situation where those who needed to be trained hadn’t been was set up because of crazy. Maybe because of a symptom or two of the crazy.”

McKay blinked several times, face completely blank. Then his entire expression twisted into what John had begun to call his how-are-you-still-breathing-my-air expression. “Has all that fluffy hair finally smothered your brain? Seriously, you’re supposed to be one of the smarter blunt objects around here.”

“Gee, thanks for that vote of confidence, Rodney.”

The faintest trace of apology danced around the edges of the scientist’s annoyed huff and it was Sheppard’s turn to wave away what had been said.

“We’re still trying to track where all Weir got to around the city, the out of bounds areas and labs and whatever that she got into and when. If for no other reason than to make sure she hadn’t turned something on that will kill us all two months from now.” McKay nodded, waving him on impatiently. “There have been sections of security footage that we can’t find. Others that aren’t where they’re supposed to be.”

A single brow rose almost in challenge. “You’re dealing with GI Joes, does it really surprise you that they’re more incompetent than my stupid science minions?”

“They’re not stupid, McKay.” Some of the military commander’s frustrations showed through as he sighed and ran a hand through his perpetually untidy hair. “We originally came out here with only three junior NCOs who had ever worked as MPs. No one had training for this kind of thing.”

John rubbed the back of his neck, voice trailing off with a gruff noise.

“I just don’t understand. It doesn’t look like there was any official assignment of an MP unit or anything of the sort. With the lack of officer corps I’m not sure what kind of force protection or security staffing was planned. Certainly Sumner hadn’t given anyone that position.” Sheppard pushed back from the table, stood and paced for a moment, then dropped into the chair next to McKay’s instead of the one he had been in across from him.

“And from what I can tell, when Weir assigned Bates to head of security for the city, she provided him with a list of tasks and priorities of her own creation. Because there was no such thing in the charter as far as I can tell. Which aside from being short-sided, doesn’t explain the job description she gave him that he has not surprisingly followed to the letter.”

The CSO’s eyes widened a little as the other man made vague hand gestures that incorporated most of the room. “No one seemed to think it odd that their patrol schedule was posted in the damn room with copies sent to the expedition leader weekly. No one had any problem being told that civilian matters weren’t something that the military security force needed to deal with. That military and civilian issues were best dealt with independently.”

The faintly amused irritation fell from Rodney’s face. “What?”

John threw out both arms with an incredulous expression. “Yeah!”

“There is no civilian group to deal with that kind of stuff. The charter was clear that all security concerns were to be the purview of the military, on and off the city.”

Somehow, watching McKay rant and rave and wave his hands erratically in the air managed to calm Sheppard rather effectively. His friend spent the next five minutes complaining about Weir’s stupidity and the plethora of errors and injustices in the way the expedition had been designed and run. By the time Rodney was done, both men were left sitting next to each other, shoulders touching, just overwhelmed by the scope of problems they were facing.

Unsurprisingly, it was the scientist who lost patience first and stalked from the room, muttering under his breath about Caldwell needing to get on top of things so he could get back to what he was supposed to actually be doing. John just rolled his eyes and yelled after him. “Team movie tomorrow. It’s your turn to host, Rodney.”

The CSO gave an absent hand wave over his shoulder, already buried nose deep in his tablet. So Lt. Colonel John Sheppard sprawled back in his chair and took advantage of the silence in the room. Rodney’s presence elsewhere was sure to be felt soon enough that the Marines who had fled the room half an hour earlier would head back to their office in the next few minutes. Yet he continued to sit there, tablets and files spread out in front of him, mind spinning back where it had been before he had been interrupted.

He had been having problems with Sgt. Bates almost from the beginning, but it had been more an attitude and respect problem than anything else. As upset as he had gotten with the NCO’s behavior in regards to the Athosians it wasn’t that he suspected them that had been the issue. Any security officer would suspect the large group of unknown, unvetted outsiders when a security leak came up.

It had been the way Bates had been assigned by Elizabeth without his input and then used that position to challenge him in every way possible without hiding his lack of respect or his inability to follow orders without argument and complaint that had been a sticking point. Not to mention the blatant way the Marine had disdained his new CO for his black mark and distrusted him for his actions regarding Sumner’s death.

John ran both hands over his face and then forced himself to start backing up all the new files and data to go back over with a fine-tooth comb in his own office. Once he had carried his tablet and the backup security laptop to his destination, he finally allowed himself to curse extensively under his breath. This was not what they needed on top of everything else. And not just because it was a fucking nightmare. It was a nightmare he didn’t know how the hell to navigate. His head fell forward in his hands, eyes staring sightlessly at the computers on the desk in front of him.

“I am not trained for this shit,” he muttered in exhaustion. Even without training, however, he had an idea how bad this situation had the potential to be and he forced himself to get back to reviewing things in an effort to determine the extent of the fuckup he would be dealing with.

His actions neither soothed nor inflamed his concerns about the security team having cut other corners. Frankly, he didn’t even know quite what he should look into, and if he didn’t know that much, how could he possibly find the answers he needed?

As relieved as he had been to be given the military command on the city, he was tempted to regret a great many of his life choices. He was definitely not trained for this kind of shit.

But Tony was.

He raised his head, hands falling onto the desktop. A second passed. Then he was reaching out with single-minded determination. Personal email accessed and new message opened, he began to type. He couldn’t ask anything specific, of course. Nothing that would give any indication of what he was looking into or why. But general questions would be fine. Simple things that any cop or investigator would know but which completely eluded him as a combat officer.

NCIS was often tasked with force protection if he remembered correctly. As long as he asked in the right way, at least some of this would be markedly easier. Well, perhaps not easier. But he was sure to screw up fewer bits with at least some kind of direction to go in.

John had a moment’s hesitation as he finished the carefully worded request for advice. It had been less than two weeks since he had received the messages about the infuriating and bizarre situation with the Mossad agent being added to Tony’s team. He knew that his childhood friend was still upset and stressed and struggling with his situation at work. He certainly didn’t want to add to the agent’s stress. But they were very basic questions. And Tony always did like to keep himself busy when he was angry or hurting.

“Fuck it,” he muttered, clicking send and shutting the laptop before he second-guessed himself. He would just have to pay close attention to the younger man’s responses and subsequent messages to make sure the involuntary Dear Abby impersonation wasn’t bothering the former cop. Not that he thought Tony couldn’t handle it either way.

He rubbed his eyes rather vigorously and let out a laugh that was anything but lighthearted. “Hell. DiNozzo could probably run this whole city, restructure the security forces, wrap up the glowing cesspool and enforce the charter without breaking stride.”

He had a sudden image in his head of his old friend skipping around the city of the Ancients, putting out fires, arresting errant scientists and Marine’s alike, all while playing the occasional prank on Rodney. John laughed harder than he had since he stepped through the ‘Gate. Then his radio beeped in his ear and he was forced to sound like a full-grown man in charge of a military contingent stationed in the middle of a hostile territory a full galaxy away from reinforcements.

Chapter Four

Tony set his empty plate aside and fiddled with his laptop for a few minutes as he tried to figure out what the hell to say about the epically crazy week he’d just had. He had to say something, of course. Knowing McKay, the man had some kind of alert on his name in the weekly email exchange their base had stateside that dumped him with every electronic mention of Anthony DiNozzo available. The scientist certainly liked to know more than everyone else, before everyone else. Especially John. So not mentioning his arrest and subsequent release could actually be more trouble than it was worth.

Even so, reliving the events was not at the top of his list of things to do at the moment. He sighed and got up to put his dishes in the sink and buy himself a few more moments before he needed to get typing. Once he had tidied the table and loaded the dishwasher and even served himself up some ice cream, he could avoid it no longer and sat back down in front of his computer.

Hey man, so, small world. Turns out our new lab tech once worked on one of my cases in Baltimore. Well, he screwed up my case by contaminating some blood samples. I reported him back in the day and he ended up getting fired. But, the point is we crossed paths in Baltimore and then he came to work here.

Apparently he had a mortal-enemy-level grudge thing going on and went super spy to frame me for murder a few days ago. Did a decent job of it too, the FBI arrested me and everything. He screwed up again, though, and the team proved it was a frame job so I am free and clear.

His fingers paused in their trek across his keyboard. The team did indeed clear him, which at certain points in the whole process, was more than he had expected. Not that he thought Gibbs wasn’t a stellar investigator or that Tim hadn’t come a long way since he left cyber crimes. But considering the skewed team dynamics since Ziva had been assigned to them, he was actually a bit surprised that it had come together the way it had.

Maybe I can trust them, he started to write, then started over again. Maybe I can trust her more than I thought. No, he thought as he tapped on the delete button with a little more force than necessary.

No matter how the case had turned out, he could not shake the fact that he had spent the entirety of the whole thing feeling like an axe were hanging over his head. The problem of course, being that the axe had not been FBI-shaped.

As much as the feebies had seemed determined to prove his guilt, as hard as they had come after him, the axe had born a striking resemblance to Ziva David. The repeated jokes at his expense throughout the investigation had not only been ill-timed but when Ziva made them, they had sounded less joking and more malicious.

Cracks about him being the kind of guy to piss off everyone he met and having too large a field of people who might want to frame him to even try and investigate had not made him feel particularly confident in their determination and commitment to seeing him cleared. And the fact that NCIS had hired a tech to work criminal cases who had been fired for contaminating evidence? Really? He had to admit, his confidence in more than just his teammates and his director had taken quite a hit.

Best not to point that out to John. McKay was sure to have a few comments on that shoddy bit of staffing as it was. And he would have a point. It shouldn’t have happened. Yet it had, and it was far from the first thing that left him wondering if he would ever again feel safe in the knowledge that his team and his bosses had his back in the field or the bullpen. Or the interrogation room, for that matter because where the hell was the offer to get him a lawyer?

He’d told Fornell he didn’t want one when he’d been questioned, but he’d also told McGeek to look up a good one in case they didn’t find the proof they needed and he’d never heard back about it. Certainly the information hadn’t been emailed to him like he’d asked. Tony ran a hand over his face. His probie had probably been too busy avoiding head slaps and following rule number thirteen.

Now was not the time to think about that, though. He still had an email to get through. Shaking his head and rolling his shoulders a bit to loosen the tension that had been there for weeks, he did his best to type out something lighthearted.

Drama drama around here. I bet you had a really slow week in comparison huh? We should just declare me the winner of the craziest week now and save ourselves the effort of judgment.

Of course, I always win because as crazy as your place might be you totally can’t tell me about it so I win by default. Still sweet though. And frankly John, I deserve it this week. The FBI holding tank was not a four-star stay, let me tell you. Crap amenities, and customer service sucked, what with the interrogation and the accusations and all. Total two thumbs down.

There, that should do it. Now, on to better things. Like the answers to the odd questions John had sent him regarding standard investigative techniques and procedures. Why the military commander of a base way out wherever, was coming to an agent in DC for tips to give his MPs didn’t make sense to Tony. But that John was coming to him for advice on anything was enough to leave him reveling in the feeling of trust and respect that was implied by his friend’s questions. And that was enough to make him forget about his drama drama. At least for tonight.

– – – – –

John was sick of reading the backlog of complaints and security files that had been making their way to his attention during their investigation into Weir and the city she ran. He was in fact so sick of it that the stern and unhappy face of Colonel Caldwell at his door was actually a relief to see. His hope of being distracted was quickly dashed, however.

“Sheppard. I noticed you hadn’t filed your report updating the security review for this week.”

The military commander was too tired to prevent the long, heavy sigh from escaping. “I haven’t completed it yet, sir. I am still going through old files. There are over 150 complaints that were filed since we got to Pegasus. Most of them are written by civilians about other civilians, but I’ve also come across a dozen already that were written by civilians about military personnel. And I’ve only gotten half way through.”

Caldwell frowned harder than he had been when he arrived. “What is the nature of the complaints?”

John wasn’t surprised that he didn’t bother to ask why they needed to be addressed, they both knew that Weir had told Bates that any civilian matters were not the responsibility of the Marines assigned as security officers. Green eyes fought the urge to roll.

Bates must have been either looking for a subtle way to defy his commanding officer – and given his hatred of John that wouldn’t be surprising – or he just had no idea what the role of head of security for the city was supposed to entail or how to do it. Since the NCO had not come out to the city with that role in mind, nor been trained as an MP or force protection at any point, that was also a feasible explanation.

Whatever the reason for the mess, John still had to clean it up. He pushed his tablet and its screen full of mind-numbing paperwork further away from him on the desk. “It’s been mostly petty theft reports and accusations of harassment. I haven’t come across any mention of outright assault as yet.”

They both winced visibly at the possibility, though the Air Force officers had served at enough bases to know such a thing was far from impossible. The older man cleared his throat and continued their conversation. “And the problem with the complaints?”

“Nearly all of them look to have been set aside without being looked into. But even the ones that appear to have been addressed in some way, well, I don’t think they were handled correctly to be honest. From what I have been able to learn about the procedures for this kind of thing, we won’t be able to properly follow through on the original complaints at this point.”

John ran a hand through his hair, letting it pause for a moment to grasp the back of his neck before dropping it heavily into his lap.

“There is no real chain of evidence, and what passes as the official statements are a mess. I can’t find any notes on what if any questioning or physical look-see was conducted at the time of complaint. Frankly, sir, SNAFU is putting it mildly.”

Steven Caldwell scowled and made a disgruntled humming sound that the other man took to be irritated agreement. But when he said nothing, the Lt. Colonel went on.

“We need, at the absolute minimum, one person who has actually been trained in this kind of thing. As far as I can tell even the couple of former MPs don’t know everything they’d need to for them to run any type of investigation, provide security, force protection, and what amounts to law enforcement for an entire civilian and military community of over two hundred people.”

Neither said anything for several long seconds. Then John broke the silence, his voice tired. “We probably can’t get the help we need on this for a while yet. And by that time, hopefully the majority of this mess will be dealt with for the most part. But we have to do stuff right from now on. And looking into stolen coffee and verbal harassment is going to be the very least of what we have to be able to deal with.”

Caldwell’s eyes narrowed as his military commander leaned forward in his seat and met his gaze head on. “This expedition was sent out with a fairly clear and extensive charter. As far as I’m concerned the content of that is just as important to monitor and enforce as the UCMJ and the civilian laws we are subject to out here. This is a fully self-contained city, Colonel. We have to start treating it as one.”

There was another beat of silence, then the new expedition leader nodded sharply. “I will speak with the SGC and the IOA to see what options we have in that respect.”

John let out a breath as quietly as he could. “If I could offer a suggestion, sir?”

The senior officer lifted a single brow in question, prompting him to continue. “I have heard a little about the position of Agent Afloat at NCIS. I don’t honestly know what the AFOSI equivalent is, but some type of similarly trained civilian with a duty oath to uphold the charter and experience with the military and the UCMJ might not be a bad place to start looking.”

Steven nodded again. “If I could officer the same?” He didn’t wait for John to nod back. “I think it is an opportune time to offer Sgt. Bates a reassignment to the SGC.”

The dark haired man couldn’t hide his wince. He and Bates didn’t like each other much, most of the military contingent on the city was aware of that. And he was certainly not pleased with the mess the security officers had made, but technically, Bates had always followed orders and done exactly what he was told he was supposed to do. He had never once completely crossed any line as far as John was aware.

Before he could respond, Caldwell gave him a knowing but unsympathetic look. “He holds you personally responsible for Sumner’s death, Sheppard. I’m going to offer to transfer him back to Earth. I seriously doubt he will request to stay here.”

John leaned back in his chair and just nodded a wordless agreement. As if he considered that the end of the discussion, Caldwell stood from the seat he had taken in front of the younger man’s desk and moved to leave. Just before he stepped through the door, he turned back.

“I will consider our meeting to be a verbal report, but I will need the proper forms regarding the situation no later than the middle of next week.”

Sheppard acknowledged the order but waited for the officer to leave before grimacing in distaste. They had worked effectively together since he first arrived, and he appreciated Caldwell’s help while he was turning into a bug, and again when Weir did her suicidal disappearing act. He did. But the man was still an uptight ass a lot of the time. He winced again, knowing that the entire city was still on edge, especially the administration. The former Commander of the Daedalus was no doubt just as overrun with mess and paperwork as he and Rodney were.

John ran a hand over his face and decided that he was in fact overrun and overwhelmed and that it was time to wrap things up for the day. Dinner had been over two hours before and he was ready to head to his personal quarters. Making good on his plans, he was sitting on the edge of his bed with a relieved sigh less than twenty minutes later. He reached out to start a movie on his laptop but decided to check his email first since the databurst from Earth had come in that afternoon.

They had almost made a bit of a game out of Rodney tracking him down to relate the latest craziness that had set off the search algorithm, so John was more than a bit surprised to open an email from Tony and discover it himself. He sat and stared at the computer screen for several long moments after reading through the message.

He stood, marched out of his quarters and down the hallway to McKay’s rooms, and activated the charm on his door with a smug kind of fury. When his friend answered his door with an impatient exclamation, Sheppard hurried inside, barely able to keep it to himself long enough for the door to close behind him.

“Tony was framed for murder this week,” he stated, only a hint of his anger showing through the glee he felt at being the one to break the news.

Watching the scientist turn to stare at him with shock and indignation was almost as much fun as the way he scrambled to his computer to read the new email with a yell. “What the hell did Tony get into this time? Damn it I knew I should have started that search program. I’m doing it tonight, Sheppard, I really am. Because your crazy friend needs a damn babysitter.”

John arched a single eyebrow, though he found himself less surprised than he should have been at the implication of Rodney’s threat. “You wrote a computer program to babysit Tony? Did you name it Jarvis?” he asked with amusement as he found a seat on the edge of McKay’s bed.

Blue eyes darted up from his screen and narrowed in the other man’s direction before flicking back down to skim over the email contents. “Oh, ha ha. Though Iron Man was totally the best one. But no, smartass, I wrote a version of the search algorithm used on the databurst to skim various databases for mentions of Tony’s name in case he follows your example and gets himself into trouble he can’t get out of.”

The Lt. Colonel rolled his eyes and waited for his friend to finish reading. He didn’t have to wait long, nor did he have to ask the other man’s opinion of the situation. Not that Rodney normally waited to be asked for his opinion before offering it. Usually he just assumed everyone needed to hear what he had to say whether they wanted to or not.

So it wasn’t the least bit surprising when the scientist stomped over to sit beside him, leaned over with an accusatory finger poking into the soldier’s chest and said, “He doesn’t have much more respect for his own life than you do, does he? ”

John glared just a little across the scant inches that separated them, managing to sound more offended than curious. “What exactly is that supposed to mean?”

McKay rolled his eyes with such enthusiasm that his friend reached out to catch him, expecting the motion to cause the scientist to fall backward onto the mattress. When the other man stayed firmly seated, John let his arm rest instead across Rodney’s shoulder as he spoke. “Aside from making jokes about being arrested and put in jail? And trying to make it sound funny that he was actually framed for murder?”

“Well, yeah. Other than that,” the soldier said almost sheepishly. It wasn’t like he hadn’t noticed. Or that, as much as he hadn’t been surprised by the use of Tony’s attempt to downplay his situation with humor, reading it had still left him a little concerned for his friend. At least, more concerned than he had already been.

Rodney narrowed his eyes, arms crossed. “His bosses actually hired a scientist that had already been fired for contaminating evidence.”

The CSO of Atlantis grimaced in clear disgust, the expression almost tempting a smile onto John’s face despite the seriousness of the topic of conversation. Not that John was shocked to find it entertaining to watch the other man stand and begin to pace as he spoke.

“So the damn retards are either too incompetent to know who the hell they were hiring, or they don’t care who they are hiring,” the scientist exclaimed with a rather large wave of his arms.

“Presumably the man used a false name but hiring someone with an assumed identity and not realizing it is hardly any less incompetent. Which for a federal investigative agency is beyond pathetic, Sheppard. It’s moronic and dumb.” The way he said the last word actually managed to make it sound the most insulting of any he had used so far. John swallowed back a smile and continued to listen. “Not to mention dangerous. Though I can’t be terribly surprised since these idiots actually thought it was a good idea to hire that ninja-bitch.”

The military commander of the city couldn’t hold back a short laugh at the by-now familiar nickname McKay had given Tony’s female co-worker. When the sound drew a harsh glare from the other man, he promptly held up both hands in mute surrender. A long beat of silence passed before the gesture was accepted and a very thorough discussion of the ills of NCIS was conducted between them.

Certainly, having Rodney’s undivided attention and a suitably juicy topic of debate drove all thoughts of regulation and charters and city administration from John’s mind. The thoughts it left were almost as stressful. Thoughts of the very real danger Tony might be in working for a chain of command that had again proven it couldn’t truly be trusted to behave in its agents’ best interests.

That train of thought probably would have been more stressful, he had to admit, if not for the fact that he was exploring it with Rodney. The view of McKay, fully worked up and defending his childhood friend – insulting language and enthusiastic arm flailing included – was far more comforting than he wanted to admit. He had a sinking suspicion that he had reached the end of his ability to lie about it, at least to himself.

As he lay in bed that night, John stewed over the idea that his oldest friend might be unsafe at his job, not because of what it was, but because of who he worked for and who he worked with. The thought spun off into a mental review of all the things they still needed to fix in the city so that his own co-workers weren’t endangered by the mistakes that had been made in Atlantis’ administration under Elizabeth Weir.

He accepted that they were under constant threat of the Wraith, and insane Ancient technology, and other unknown craziness inherent to Pegasus. But Lt. Colonel John Sheppard suddenly could no longer stand the idea that they were at risk because of what amounted to simple greed and arrogance. He wouldn’t let his men die for Weir or anyone else. He wouldn’t let the civilians die, even for the next big discovery for want of some caution.

He wouldn’t let Rodney die for any reason at all if he could help it.

– – – – –

Typing up his report and all the other paperwork that came with being SFA was hard enough with an arm in a sling, but doing it while pretending not to listen to Ziva provide Tim with a revisionist history of what had happened at the dock was almost impossible. The fact that he was a few hours overdue for his pain medication because he hadn’t been able to take a break for lunch and wasn’t willing to deal with the nausea if he took it on an empty stomach didn’t help either.

If not for the combination of irritants, he probably would have had the patience to ignore her or the strength to push through the constant ache and pull in his arm as he shifted to peck away at the keys with his left hand. As it was, however, Tony couldn’t help but interrupt.

“Why don’t you type up your report of the incident, Officer David, instead of narrating for the bullpen? I’m sure Agent McGee has a few bits of paperwork to do as well.”

Both junior agents shot him a glare but he had become well used to ignoring those over the last month and simply continued his reports. It took about all of his focus, anyway, to avoid grimacing as he pulled on the stiches. He ignored his growling stomach and after he finally gave in and took the pain meds, he ignored the queasy sensation that followed. At least the pain relief allowed him to get through the afternoon.

Getting through Ziva’s report when it was finally sent to him was another matter. He had half expected her to leave out the small fact that when she fired the shot inside the shipping container that she had done so despite him telling her not to. So that part didn’t surprise him. She tended to think that something he said was not her job to cover in her report. Never mind that she had expressly ignored a direct order from a senior agent while in the field. What he had not expected were the various places she had implied that she hit some of the shooters outside the container or that she called his injury a ‘minor scratch as the result of a ricochet bullet.’

Granted, he had been shot by a ricochet. The bullet had been fired inside a closed metal container. Of course it ricocheted. Which was why he had told her not to fire in the first place. But calling his bullet wound a scratch when talking in the bullpen was bad enough. Implying she shot more than one of their attackers in an effort to save face in front of the other agents that night was bad enough. And unprofessional as hell. Lying in such a way to cover up her mistakes in an official written report when it was clearly disproven by the forensic analysis of the scene that had already been turned in? That was way past unprofessional.

With some of the most precise clicks of a mouse he had ever made, he sent the report back to her for corrections. Tony was entirely unsurprised when it was only minutes before the woman was shooting him a dirty look from her desk.

“You have been yipping at me all day to send my report and now you do not want it?”

“Uh, I think you mean yapping, Ziva,” Tim corrected with a curious glance back and forth between his teammates.

Tony ignored him and fought to keep his voice level and calm. “I do want the report, I in fact wanted it two days ago when it was due. However, I need it to be accurate before I can actually file it.”

Ziva scoffed, though the dismissive sound did not quite match the anger in her glare. “There is nothing wrong with my report, you are just trying to buy yourself time to finish your own no doubt incomplete work. At Mossad-”

He didn’t even let her start to explain what they did better at Mossad, he simply did not want to hear it. Her insubordination was past his tolerance level. Her attitude was getting bad enough and having enough of an effect on Tim, not to mention the team dynamic. But not listening to him in the shipping container could have gotten them both killed and had gotten him shot. Tony continued to keep his gaze on his own computer.

“As SFA I am responsible for closing out files when a case has been completed and I cannot do that with incomplete or inaccurate reports. Since your report does not include a full account of what happened at the docks and is contradicted in several places by the forensics, it is both. Correct and complete your report, Liaison Officer David, and submit it to me by the end of the day.”

He heard her chair roll back suddenly and smack into the file cabinet behind her desk but did not turn away from his screen. Which is why Gibbs’ sudden appearance actually managed to startle him slightly.

“Shut it. Both of you. Ziva, give me the report.” Gibbs turned away from the newest member of the team, conveniently missing the smug little smile she shot in Tony’s direction as she moved to print the document. While she maneuvered around a suddenly studious McGee to get to the printer, the team lead stalked over to his senior field agent’s desk with a scowl. “DiNozzo. Yours too. And get back to work.”

Tony’s hand wanted to shake as he gathered up the almost complete file and handed it over. He forcefully suppressed the urge to point out that he hadn’t been the one complaining and avoiding work, that compiling the file was his job, and that he could hardly get back to work as he had already been working.

He suppressed it so forcefully, in fact, that it felt like it was rattling around in his chest like a berserker in chain-mail. The sensation was disturbingly similar to how it had felt when the pneumonia from the plague began to drown him in his hospital bed under those blue lights.

But he didn’t say anything, just handed over the file and watched the former Marine take Ziva’s papers and go back to his desk. Green eyes focused back on his screen, though he heard the rustle of pages and assumed the older man was reading through all the reports. But if Gibbs finished them he didn’t say it before they left for the day two hours later. Gibbs didn’t say anything the next morning or the one after that. If his boss had noticed the glaring inconsistencies between Ziva’s report and every other report in the file, he didn’t say anything to, or in front of, Tony.

After the second day of cold cases and business as usual, DiNozzo began to wonder if Gibbs had bothered to read the reports after all and had just filed everything himself instead of giving things back to his SFA to do. Or maybe, he thought as he caught a cab home another silent day later, maybe he’d thought it was not a big deal for their liaison officer to be inaccurate, even dishonest. Maybe it was only okay because it was their liaison officer.

Perhaps, Tony mentally expounded as he glared at the sling that prevented him from driving himself to and from work, Gibbs saw the differences between reports but still believed her version over the others and just closed the file, forgetting about what he thought to be a minor squabble between teammates.

Pushing his bag higher on his good shoulder, the tired agent struggled to get his door unlocked and himself into the apartment before he dropped everything in the hallway and trudged over to his waiting couch. Realistically, the radio silence from Gibbs on the subject was probably a combination of all of the above.

The older man had not, after all, questioned her version at the time, despite his stiches and the doctor requiring him to be on desk duty. Certainly neither of those would have been the case if it were just the minor scratch she had claimed. Yet the taciturn agent had acted like Tony had just been milking it by staying in a sling and out of the field.

So he could have both believed Ziva and not bothered to read the reports. Most likely, if he had bothered to read it and noticed the differences between his account of the incident and Ziva’s, Gibbs would have demanded that Tony ‘fix’ his. Then again, he could have read them, noticed, asked Ziva about it, believed whatever spin she put on things, and let things go.

Covering his face with one hand, Tony groaned into his palm. He had to stop thinking about it. Obviously it was in Gibbs’ hands now, literally. There was nothing else he could do other than confront his boss about the reports. And not only did he know better than to question the man about such a thing, he was just too damn tired. He felt like he spent every minute of his workday on guard and picking a fight with the former Marine was just not an option.

Though what exactly his options were, Tony was beginning to wonder. While he gave that question some serious thought, he began compiling a report or two of his own. Just in case.

– – – – –

John glared at the screens of the two tablets and one laptop that were all open on the desk in front of him. He really should feel relieved to be done with the mess that had been the security office. He knew that was how Caldwell felt having finished reviewing all the administrative decisions from his predecessor as well as re-vetting the control room staff. Rodney had talked for two days about how happy he was that he had finished going through all the previous experiments and then the work of the scientists assigned to field teams. Beckett certainly beamed at having completed the review of the psychiatric department and conducting updated health evaluations for everyone in the city.

Yet John almost wished he were still mired in the video footage and security reports. The urge he felt to toss the computers he had been working on at the heads of his fellow senior staff members, however, had only grown since he had started his next assigned task. That he was the only one who seemed to loathe his current allotment of damage control almost made his frustration worse.

The CSO seemed resigned to reviewing all actions and experiments and other work and conduct of the various department heads in the sciences. The expedition leader appeared content with having claimed jurisdiction over the military members of field teams and the review of all previous mission reports. And Beckett was all smiles having moved on to evaluating the infirmary staff.

At first John had been fine with that division of labor. He understood it would be difficult for him to accurately review his own team’s reports, after all. The problem was, it left him with reviewing the reports and conduct of the CMO himself. Particularly the doctor’s experiments.

For all that it distracted him from the last email from Tony – which had painted a progressively bleaker picture of his position at NCIS – his assignment was a problem. At least if he had been reviewing the science department heads he would have understood most of the math involved in their work. He didn’t understand hardly any of the science behind the stuff coming out of the infirmary. Sheppard ran a hand over his head, sending his hair into even greater disarray, and let out a long sigh. Then he reached up to activate his comm. “McKay, can you join me in my office please?”

He was inordinately proud of the fact that his voice sounded normal, even polite, as he finished the request. Rodney, of course sounded irritated and short tempered when he snapped out that he would be there soon. But for Rodney that was normal, so maybe he should be proud of him too. Certainly, he was relieved to see the other man at his door fifteen minutes later, despite his greeting.

“Well, what do you want, Sheppard?”

John scowled for several seconds without saying a word. Then motioned his best friend to step through the door and mentally prodded it shut behind him. McKay responded by crossing his arms over his chest with a huff.

“Come on, I don’t have all day here.”

“We’re all on deadlines, Rodney. You aren’t the only one who has to finish reports for the next databurst, you know. I have to get through this medical… stuff. But as much as you don’t want to admit it, medicine is a science, and you are the CSO.”

Said Chief Science Officer rolled his eyes. “Yeah, so? Carson and his stupid science, is your problem right now. Caldwell said so. What does that have to do with me?”

“One of the things we agreed to look over was how the charter has been and is being followed.” John glared briefly at his own hands where they lay clenched together on his desk.

Going over the ways the charter had been ignored when his previous actions had been reviewed on Earth had been no picnic, and the new orders he and Caldwell had each received from the SGC had been very explicit about how that would work between the military commander and expedition leader going forward. And hadn’t that been a fun conversation to have with his superior officer, the Lt. Colonel mentally sneered.

He cleared his throat and looked back up at Rodney to find the other man grimacing. No doubt McKay had had just as much fun going over his own actions with Caldwell while John himself had been on the outgoing trip on the Daedalus.

“The charter gives the CMO acting authority in any medical situation, but all medical research is considered under the authority of the CSO. That’s you, Rodney. So if I want to know if the charter has been violated, I kind of need to know what you okay’d and what you didn’t and what you knew about medical research stuff and when you found out.”

He also, of course, didn’t understand the majority of the medicine and science being discussed in the various files, but he was sure he didn’t need to point that out. Certainly not to Rodney.

The grimace turned to a pout and McKay dropped into the chair in front of his desk with a heavy sigh. “Fine, fine. Get on with it.”

Sheppard raised a single brow at the other man. After a moment, Rodney’s shoulders drooped slightly and the stubborn irritation on his face lessened and was replaced by a tired resignation. “What do you need to know?”

“Why don’t we start with the ATA gene research.”

“I thought we already talked about that before.”

“I have to write up a formal report, I can’t just use what I remember from an informal conversation with you months ago.”

“Alright, alright. Carson asked me if I wanted to be the first to get it here. We’d only been here a few days at that point and I hadn’t had time to read all the reports I got from all the science departments and medical research. So I didn’t realize at the time that he meant the first human trial. I had a few questions at that point, side effects and such, not that it mattered much since he gave me the shot before he actually answered me.” Rodney rolled his eyes.

John nodded, remembering most of that from before. Not that hearing it again wasn’t still just as infuriating. “You didn’t get any reports on the gene research before we got to the city?”

McKay cleared his throat. “After I was given the position of CSO, Elizabeth informed me that while I was expected to set up the sciences for the mission, I would not actually be the Chief Science Officer for the expedition until we arrived in Pegasus. Therefore, she would be overseeing the only ongoing research project being conducted by the future CMO. Apparently, the ATA project would be used by the expedition but was still under the auspice of Area 51 until Carson left the planet.”

John’s eyes narrowed slightly, that much was new. But he refrained from responding and instead nodded, remaining silent while he made a few notes on the tablet in front of him. When he was finished, he took a deep breath and moved to the next item on his list. It was an hour before they had gone through all the questions that his review had given him and then all the questions that had arisen from them. When they finally finished, John ran both hands over his face with a sigh, leaned back in his chair, and cursed under his breath.

Rodney summed it up for them both with a huff of impatience. “It’s a damn stupid mess.”

“Yeah, I got that. The question is what are we gonna do to clean it up?”

The scientist crossed his arms in front of him with jerky motions. “You want to remove him as CMO, don’t you?”

“Let’s not get ahead of ourselves.”

“Why? It’s what you’re thinking, isn’t it?”

John let out a long sigh, rubbing at his eyes as much to relieve the ache there as to cover the sight of Rodney’s distressed expression. “What I’m thinking is that the charter has been largely treated as a list of suggestions rather than a code by which we all agreed to operate. And we can’t allow that to continue. A senior member of the expedition cannot be allowed to repeatedly ignore protocols and chain of command the way he has.”

“Gee, really? And here I was hoping that he would keep leaving me completely out of the loop and ignoring me any time I tried to tell him that an experiment was a stupid, stupid, idiotic idea.”

Sheppard pinched the bridge of his nose, wondering if there was any chance of warding off the headache that he could feel forming. He certainly didn’t feel like swinging by the infirmary for an asprin at the moment. Then again, by the time he was done with this conversation, he figured he might need something a lot stronger than asprin. Maybe by then he would be willing to risk it.

“I never said that I wanted to fire him.”

Blue eyes glared at a spot just over John’s left shoulder. “Really? Because that’s certainly what it sounded like to me.”

“Well, that’s not what it was! Damn it, Rodney.” The military commander rubbed the back of his neck with enough force that the skin was actually a little sore when he pulled his hand away a moment later. “I know you consider Carson a friend. So do I. But we can’t just ignore what’s happened. We can’t let it happen again.”

“I’m not ignoring anything. And I certainly didn’t let anything happen the first time. I know I oversee the medical research as CSO, okay? I know that.” Rodney pushed himself away from the desk and stood, beginning to pace in the small confines of the office with sharp, jerky movements.

“I’m a fucking genius. You don’t have to spell this out for me. But I have a lot of responsibilities around here. I do about three-dozen jobs every day. I oversee every science department on the city, and in case you missed it, we have a lot of scientists around here. And most of them are even more stupid about experiments and research than Carson; research and experiments that pose a much more direct and physical threat to the city. That’s a lot of damn things to personally check on almost every day so I can watch and make sure the idiots don’t literally blow us up with their remarkable incompetence.”

Something in John tightened as he began to see where his friend was headed. For all that Rodney came across as arrogant and self-centered, he knew the scientist took things to heart far more than he was given credit for. He knew that his friend took his responsibilities to his subordinates seriously and considered it his job to protect the city and everyone in it. John sat up a little straighter and opened his mouth to cut off the angry rant, but the CSO took no notice of him, and simply continued on.

“I have a pretty full fucking plate, Sheppard. So, yeah, I should have read more than just the summary before I let Carson convince me to let him try and help them create the drug on Hoff. But I was busy with about forty-seven other things and I didn’t realize I wasn’t given all the data at the time. Not to mention I didn’t have the time to review everything before the trial was conducted. Which is why I told you then that I wouldn’t have been on board with those last phases of the experiment.”

He finally had a chance to get a word in edgewise when the scientist took a deep breath to, presumably, finish at an even greater volume. “Yes! I know that, McKay. We both talked about that shit before we filed our complaints. Both of which were dismissed by Weir at the time, as I’m sure you recall.”

“Of course I recall,” Rodney agreed with a sneer. “I also remember that, right before she dismissed our complaints, that she told us both that she had spoken to Carson at the time and given her approval so our disagreement was immaterial.”

The scientist continued to pace, gesturing with his hands the way he normally did when he was aggravated. “I should have specified that no more research on the Hoffan drug was to be conducted, though. I just never thought he would continue, so I didn’t ask about if he was. But I know I should have been more proactive with my oversight of the situation considering how he tried to convince those people that they should continue trying to make the drug safer before trying it. I should have told Carson not to attempt to improve it after the fact. Maybe if I had specifically told him that-”

John stood quickly enough that his chair nearly upended as he cut off the other man’s ramble. “Whoa, whoa. That fact that Beckett kept working on the drug after that clusterfuck is not your fault. So don’t even go there.”

“I know you think like a soldier under all that ridiculous hair. I know how soldiers think of chain of command and all that. All research is under my command so that makes-”

The soldier in question moved around the desk and stepped directly in his friend’s path, forcing him to stop both physically and verbally. “Bullshit. You hardly stood by and let them do whatever they wanted.”

He reached out, grasping the wildly gesturing hands, holding them still as he went on. “I know you sent a formal complaint to Weir about not giving approval on Hoff, same as me. I know you registered another formal complaint with Weir just like I did after the bug thing. I read the report you sent the SGC about Weir approving the retrovirus research without clearing it with you.”

Rodney scowled fiercely, jaw set and teeth clenched, though he didn’t pull his hands from John’s grip. “I never would have approved that. It was a stupid idea. And what’s worse, it’s not even good science. Stripping Iratus DNA from the Wraith is dumb. It would take months if not years of dedicated experimentation to do correctly, not to mention it would require live Wraith DNA to work from. Which means a live Wraith here. Again. Which is so far beyond a good idea even my substantial brain can’t comprehend it. And even if it eventually worked in a lab, it has no actual real world application.”

Sheppard squeezed the hands he still held, his voice dropping in intensity and volume. “I am aware of the limitations of the retrovirus concept, Rodney.”

McKay took a long, deep breath and nodded. “Right. No, of course you are.”

“And so is Carson. Logically, he must be. Yet he clearly plans to continue his research. He submitted plans to Weir for experiments, including ones on live Wraith. And she approved them. He’s continued to work on it, even after Caldwell took over. He hasn’t sent you a single report or asked for your approval. That cannot be allowed to keep happening. We have to do something. If we don’t, the whole city could pay a price for it.”

The CSO’s shoulders slumped. “I know that. I get it.”

The military commander of Atlantis loosened his hold on the other man’s hands, letting them go when Rodney pulled them away to bury his face in his hands for several long seconds. John got it too. He knew McKay considered Carson a friend. And he knew that the snarky astrophysicist had never really had all that many of those, so the ones he had meant that much more to him. But there was nothing he could say or do that would improve the situation. They both knew that they could not afford to let the doctor continue to operate the way he had been under Weir’s leadership.

He wanted to make it better for Rodney, wanted to reach out and take hold of him once more. But he knew that he couldn’t. For multiple reasons. The least of which was that blue eyes had lifted to meet his own.

“What did you have in mind, Colonel?”

John swallowed his grimace at the use of his rank. His face fell into the familiar expression he knew looked calm and a little amused no matter how he actually felt. “I’m going to recommend to Caldwell that we institute a very clear protocol for medical research to be submitted to you for approval. I think a strict oversight committee could handle a lot of the review so you don’t have to go over every bit of it yourself, but ultimately, you need to be directly in charge of research and experimentation going on in the infirmary.”

He resisted the urge to rub at the back of his head as they retook their seats and instead focused on remaining outwardly composed as they hammered out a few details so he could start his next set of reports for Caldwell. He waited until Rodney had stomped out of the room to go meet with Miko before he let out the heavy sigh that had been waiting to escape.


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Sunfire

I have been writing fanfic since I was twelve and despite my love of the source material I have found plenty over the years to twist to my own purposes so this theme is going to be a blast. I love turning things on their head and looking at canon from a completely different direction and making it totally different without changing the core.

One Comment:

  1. Poor John and Rodney sweetie! Poor Tony! I am hoping the SGC snags him up soon and sends him to Pegasus! He will be a much welcome relief to a lot of people!

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