When The Levee Breaks – 1/3 – halestrom

Title: When The Levee Breaks
Author: halestrom
Fandom: Stargate: Atlantis
Genre: Drama, Episode Related
Relationship(s): Rodney McKay/John Sheppard
Content Rating: NC-17
Warnings: * No Mandatory Warnings Apply
Word Count: 83,540
Summary: Six months after the events of Doranda, John receives a wake-up call that changes the course of events in Atlantis for everyone involved, for better or for worse. While John deals with his rude awakening, some friendships are made stronger, and some are broken. He just hoped he woke up in time for him to fix mistakes before he loses the one thing he can finally admit he wants.
Artist: SpencnerTibbsLover



One

“McKay fired Radek.”

John blinked, wondering when he had ended up on his back staring at the ceiling. He could feel the throbbing on the back of his head, and it took him a few seconds to catch up on how he had gotten there. He had been discussing new security plans with Lorne to deal with pods that could potentially host an Alien consciousness that could take you over when Lorne had gotten an email. John had been sitting at this desk, feet propped up and balancing on two legs like every teacher had told him not to. He could picture them crossing their arms and raising their eyebrows as if to tell him, ‘I told you so.’

He groaned and rolled to the side, ignoring the dull ache spreading across his shoulders as he pushed himself up to his knees. He raised his head and rolled his neck, catching sight of Lorne.

“Sir?” his XO asked, peering down at him, his face unimpressed. Lorne’s unimpressed face was something John was becoming more accustomed to the longer Lorne was his XO. He rubbed the back of his neck and bit back the noise he wanted to let out.

“M’fine,” he wheezed, standing up and hiding the wince as he bent to pick up the chair. He wasn’t 100% sure he was fine, but he could feel his toes, and that was good enough for now. Sitting down, he pressed a hand against the back of his head before looking at his palm, checking for blood before looking over at his XO.

“Did I hear you right?” he asked, keeping his feet and the chair’s legs planted firmly on the ground as he slouched back. “McKay fired Radek?”

“Yes.”

John considered himself an easy going guy. He had to be as the CO of Atlantis; they dealt with a lot of weird shit, even for the SGC. During the month stay on Earth after the first year, Carter and Mitchell had dragged him out to get him drunk before telling him how weird Pegasus was with every story. It hadn’t been comforting coming from two members of SG-1.

But McKay firing people wasn’t unusual, and John frowned at the concerned look on Lorne’s face. “What’s weird about that?” he asked carefully.

“It was done formally, termination of contract and everything,” Lorne read from his tablet.

John stiffened a little at that. A formal firing was unusual, especially in the science department. It was hard to fire people for misconduct when they were exploring uncharted waters. They really had to fuck up.

“Why?” John asked, feeling his throat tighten.

Things had been tense since Doranda between him and McKay.

A small part of him knew he wasn’t helping, but he ignored it. He was having a hard time getting past Rodney using their friendship and almost killing them both in the process.

John had limits to his patience, and in the wake of Doranda, he still felt angry, even months later. There was a ball of rage sitting right in his gut that made him want to fight every time he was with McKay. It kept the logical side of him quiet, and as far as he was concerned, he was entitled to his anger and rage.

“Dereliction of duty,” Lorne continued to read. “Failure to follow protocol, failure to comply with proper procedures. Apparently, he also read classified materials.”

John frowned. “Radek?” he asked just to make sure it was the right person. “Radek Zelenka, from the Czech Republic.”

Lorne looked up and nodded. “Radek’s the one who emailed me.”

Lorne’s tablet dinged and he looked down, frowning. “Or maybe not?”

“What?”

“It’s from Radek. He says to watch the tapes from the Science meeting that just ended. It’ll explain everything. And to watch out for McKay. He’s on the warpath.”

There had been a few times when John had seen McKay on the warpath, and when it wasn’t directed towards him, it was impressive to watch. McKay was loud and had no patience, but he wasn’t outright mean most of the time. His insults were always based on people’s work and never devolved into cruel or petty remarks like some people did. It was why his scientists stayed with him. He might call them an idiot for switching the wrong crystals when they knew better, but he would also absolutely back them up if someone fucked with them.

John had never been in Rodney’s sights, and he was surprised to find himself a little nervous.

“Bring up the meeting,” he said, rubbing at his temple, waiting for Lorne to bring it up.

Suddenly, the door to his office slid open with what John swore was an echo of a bang. McKay stalked into the room, holding a sheaf of papers. For a second, the sight of paper was so incongruous with Atlantis that he felt transported back to Earth, only to be brought back as McKay slammed them down on his desk. McKay leaned over, looking pinched around the mouth.

John forced himself to stay calm and where he was, slouched in the chair, keeping ahold of his laissez-faire attitude with all the skills life had given him. “McKay. What’s this?”

“A copy of my birth certificate.”

John blinked. Of all the things he had been expecting, that hadn’t been one of them. “I didn’t think we were at a point in our relationship where we exchanged papers.”

John saw Lorne wince out of the corner of his eye, and John hid a wince of his own. Antagonizing McKay right now might not be the best idea. But considering how calm the other man sounded, John didn’t think he could make whatever bug was up McKay’s ass worse.

McKay rolled his eyes. “Do you think I am a recalcitrant child?”

John was going to get whiplash from this conversation. “Uh…no.”

It sounded more like a question than he had wanted it to, and it didn’t go unnoticed by McKay if the tightening at the corner of his mouth was any indication.

“Are you sure? Because for the past four months, you have been laboring under the misapprehension that I am a spoiled child who needs to be managed otherwise he’ll lose all of his favorite toys,” McKay snapped, leaning forward a little bit more. “I am done with it and your attitude. I am an adult. I make my own choices for good or for bad, and I stand by them.”

“I suppose they’re only bad choices 5/6ths of the time, so that does give you some good choices.”

John didn’t need to see Lorne’s face to know that that had not been the best choice he could have made.

McKay’s face, if at all possible, seemed to still even more. “Even now?”

“I said you would need to earn my trust back,” John said, trying to get the upper hand back. He felt like he was still sprawled on his back, and Lorne was looking at him with a stoic resignation that made John uncomfortable.

“I shouldn’t have had to.”

The words were soft and filled with loss and determination, and it made the small part of John that he had kept pushing to the side ache with something he couldn’t name.

“You used our friendship to get me to change Elizabeth’s mind for that insane plan,” he said, sitting forward again, still trying to get the upper hand. “You abused my trust to get what you wanted.”

McKay snorted and rolled his eyes. “Do you know they made me the CSO?”

Another whiplash of a conversation. “Because you’re good at your job.”

There were two moons. Pegasus potatoes were pink. McKay was good at his job. For all of John’s issues with him, he knew that.

“Exactly. I am good at my job. I am fantastic at my job. And I have earned the right to be proud and egotistic regarding my work because I have excelled and continued to excel in almost everything I do. I work hard at making sure I am kept abreast of everything in my department, and unlike you, I don’t foist everything I dislike onto my second in command. I do my job.”

John bristled at the insinuation, and he opened his mouth, but McKay barreled on.

“Do you think that the situation with Doranda was something I planned? Do you think that I brought us there and went ahead because I thought it would end up like that?”

McKay fell silent, and John waited a moment before he reluctantly shook his head. “No.”

McKay opened his mouth, and this time John beat him to it. “I think you pressed ahead because you’re scared. You’re scared, and you’re egotistical, and you were so focused that all common sense went out the window.”

“You’re fucking right I’m scared. I’m terrified. The Wraith are terrifying, and if you don’t think that they are, you need to resign your commission. There’s a difference between insane plans and insanity, and anyone who looks at the Wraith and isn’t terrified of them needs to leave because they’re not someone I want leading the military,” McKay snapped back. “As for my ego? Yes, I let my pride blind me. And I apologized to Radek for that. He is the only person I needed to apologize for that part of the whole situation. He is the only person who my ego ran roughshod over.”

“The only person?” John interjected, feeling anger rise. “You asked me to trust you, and I did, and look where it got us.”

“I asked you to trust me because I thought I was right, and I thought you were my friend, and I thought I had earned it. I thought I could do it,” McKay snapped back. “I apologized to you for that, and that should have been enough. I made a mistake, and the outcome wasn’t out of intent. None of us, not even Radek, could have foreseen the destruction that happened. It was unprecedented. Science fails. Science fails all the time; that is the whole point of experiment and observation. So we can learn from our mistakes.”

John could feel his temper fraying in the way only a few could manage, and McKay had always been at the top of the list. “So what?”

McKay was silent for a long moment before he stood up straighter and reached out with one hand to tap the pile of papers with an elegant and scarred forefinger. “You had a right to be mad at me but making me work to regain your trust when it wasn’t something that I should have lost in the first place is childish and immature. I don’t know what game you and Dr. Weir are playing, but I will not let you win.”

Wait. What?

McKay carried on as John tried to keep up with what he was saying.

“I have been playing this bullshit political game since I started college, and if you think for one second, I am going to allow you or Dr. Weir to force me out of Atlantis, you’ve got another thing coming. I earned my place here. I didn’t stumble onto the program like you did, and I didn’t bribe and cajole the IOA as Dr. Weir did. I earned my place. Every hard-fought mile. And I will not be forced to the side because the two of you got your feelings hurt.”

McKay leaned over, and John had the sinking feeling that when Radek had said warpath, he had meant a hurricane, intent on the destruction of anything in its path no matter the cost.

“I am not leaving. I am here,” McKay said, slowly reaching out to slide the top paper to the side before tapping the second sheet. “According to this Charter, Dr. Weir cannot fire me. She can only recommend my termination. The same way she cannot fire you. She has no control over the science division the same way she has no control over military matters. So whatever fucking truce you two have had, whatever you’ve been doing to try and compel me to agree with you two or to force me out, ends today. I am not leaving, and I am not going to be treated like a spoiled child.”

With that, McKay turned and left the room in the same whirlwind as before, with John and Lorne watching him in shock.

It took a few moments before he managed to get ahold of himself enough to look at Lorne, who looked as shell shocked as John felt.

“What the fuck?” he asked softly, slumping back into his chair and rubbing over his chest, wondering if he needed to go to Carson and get it checked out and see if his ribs were okay. His chest hurt, and he wondered if he had hurt himself more in the fall than he had thought.

Lorne opened his mouth to reply, only for the door to slide open, and Radek walked in, his whole posture screaming exhaustion. He took one look at the two of them and dropped into the spare chair. “I see Rodney has been by.”

“What the fuck happened in that meeting?” he demanded, still stuck on the idea that McKay thought he and Elizabeth were in on some plan to make him leave Atlantis.

Radek pinched the bridge of his nose. “Watch the recording, skip to 0930 or so, is when it began. Words cannot do it justice.”

Lorne was ahead of John and already walking around to set the tablet down and press play. John leaned forward, bracing his elbows on the table as Lorne leaned down next to him, both of them watching intently. The camera was in the corner of the room, looking directly at the table, and from the angle, they could see both Elizabeth and McKay in profile.

John watched as one of the scientists stopped speaking and Elizabeth leaned forward, her hands clasped as she looked around the table. “Thank you all for your updates, I appreciate the hard work you’ve been doing.”

McKay stayed silent but looked up, face just as blank as it had been when he was yelling at John.

“I know you’re all doing your best, and as I have said at every meeting, I appreciate it,” she continued, smiling around the room. “Now, onto other business. Dr. Zelenka, do you have anything to add?”

Radek in the recording squirmed and shook his head. “No, I do not.”

Elizabeth frowned. “Nothing?”

Radek shook his head again.

McKay cleared his throat. “That’s enough, Dr. Weir. Dr. Zelenka will no longer be hacking my computer on your orders.”

John felt his breath catch as everyone on the screen froze. He heard Lorne’s muttered ‘oh shit’ and he folded his hands in front of him to avoid rubbing at his temple.

Elizabeth had the good grace to look a little sheepish before her shoulders squared, and her face took on the stubborn cast John hated. “I think under present circumstances you can understand my reticence regarding your work. I merely want to make sure we don’t have another incident like Doranda.”

McKay looked up and looked right at Elizabeth, and even though John could only see half of his face, he could see the simmering anger that switched to cold fury. “Perhaps four months ago, but that time has come and gone. And he will no longer be looking at my personal work.”

Elizabeth smiled, but John could see how strained it was now. “Dr. McKay,” she began.

“No,” McKay cut in, voice hard. “It ends today.”

McKay turned, and John could see his face fully for the first time, see the same resolve he had seen on his face when fighting the super Wraith. “Dr. Zelenka,” he began only to stop and take a deep breath, and that resolve firmed up even more as he picked a piece of paper and slid it across the table to Elizabeth. “Effective immediately, you’re fired.”

As a whole, the room gasped, and Elizabeth blanched. “On what grounds?” she demanded.

“Dereliction of duty. Failure to follow procedure. Failure to comply with procedures. Furthermore, when you return to Earth, you will be facing a formal hearing for reading material that is classified above your security clearance.”

The room was silent, and John could see Elizabeth pale and swallow. “Dr. McKay, this is,” she began only to stop. “This is extreme. He was following my orders.”

“I know, and I will also be filing a formal complaint against you for international espionage,” McKay said, and John didn’t think Elizabeth could pale even further, but she did.

“Dr. McKay. All Atlantis personnel have the same clearance for material from this base,” she tried.

“Yes, they do. But I also do work on the side for both Canada and the IOA, as you know, because you helped me iron out the specifics of my contract in regards to that,” McKay said. “The SGC is well aware of my work for them and understands it’s classified to each country. My personal computer is the only place where that information is allowed, and anyone caught breaking into it, is in fact, committing international espionage.”

McKay’s voice was devoid of any of the emotion that John usually associated with the man. He was calmer than John had ever seen, and even though their relationship was strained, John didn’t like it. He didn’t want to see McKay as calm as he was. It was unnatural.

“Dr. Zele–”

“Dr. Zelenka signed the same Charter we all did, which discusses the respective security concerns of individual countries. No member of the Expedition is allowed to read those files unless they sign an NDA from that country. I do work for the US that is outside of the SGC. I also do work for Canada and England and have helped out China, Russia, and France at varying times. Those are just the countries who are part of the IOA,” McKay continued, matter of fact.

“You can’t fire him,” Elizabeth tried one more time. “I won’t allow it.”

McKay leaned forward then, elbows on the table and hands clasped. “What the fuck do you think you can do to stop me?” he asked softly. “You can’t fire me, you can recommend my termination as per the Charter, but you have no control over my appointment on this mission. I report to you for streamline sakes, not because you are my boss. The IOA is in charge of my appointment, and the IOA will be in charge of my removal, and you and I both know they won’t remove me.”

The room was deadly silent, and even John felt his breathing slow as McKay continued. “You have no control over what happens in my department. You can make suggestions, and I might take them under advisement. But at the end of the day, I run them how I please. In the same way that Colonel Sheppard is in charge of the military. We are not your subordinates Dr. Weir; we are your equals. And you seem to have forgotten that.”

John started a little bit, eyes widening, surprised at that, and he glanced over at Radek, who nodded his head tiredly before his eyes shot back to the screen.

“Colonel Sheppard agrees with me that you need to be monitored to make sure another Doranda doesn’t happen,” Elizabeth said, trying to get back onto even ground.

John let out a long low groan, reaching out and hitting pause, needing a moment as he dropped his head onto the table.

“This is not happening,” he muttered. “This is not happening.”

“It is,” Radek said softly.

“Well, shit,” Lorne muttered.

John raised his head and looked at Radek. “She did just imply that I was in on your spying or whatever the hell it was, right? I didn’t even know about it!”

Radek nodded. “Ano. Rodney has known about my snooping since she ordered me to, and he was okay with it for the first week or so, but she has not backed off.”

“You actually looked?” Lorne asked sharply. “There’s protocols in place for personal computers.”

“No,” Radek snapped. “Am not stupid, I know full well what work Rodney does for others, do not want any part in that mess, but she kept pushing, and if it wasn’t me, it would be someone who did not realize, and that could get them in serious trouble.”

John sat up and rubbed his hands over his face, making a note to ask Lorne about personal computer protocols later. “How much worse does it get?”

Radek winced. “Keep watching.”

John groaned and reached out to tap the play button, feeling like he’d rather face down a Wraith right then.

The room was silent after Elizabeth spoke, and then McKay leaned forward. John could see the tension in his shoulders, the sudden rage that seemed to build even through the screen. Everyone else could also see it as they not so subtly leaned away from McKay.

“I don’t know what game you and Colonel Sheppard are playing,” McKay said, sounding like he was forcing the words out. “But it won’t work. I earned my spot on this Expedition, and I will be damned if I am forced out. I am the Chief Science Officer. You cannot fire me, and if you think this is the first time a bunch of stuck-up idiots has decided to try and put me in my place, you are wrong. I’ve been dealing with this bullshit since I was fifteen and defending my first Ph.D., so trust me, Dr. Weir, there is nothing short of murder that will make me leave this Expedition, do I make myself clear?”

Elizabeth seemed as taken aback as John was before she narrowed her eyes. “No one is going to murder you,” she snapped, her voice at odds with the pleased look on her face. “Don’t be paranoid.”

McKay let out a mirthless chuckle. “Dr. Weir, you just told me that both you and Colonel Sheppard have been working together behind my back along with Dr. Zelenka to look into my classified files. Do you think you are the first duo or trio, I suppose, to resort to murder when the target doesn’t give in?”

John let out a stuttered breath, wondering how in the fuck McKay had gone from ABC to 987. “Oh my god.”

“Rodney, you’re not going to fire Radek; we both know this,” Elizabeth tried as McKay stood up.

McKay stopped and looked at Elizabeth for a long moment, pressing both hands on the table. He dropped his head down between his shoulders for a moment, the silence in the room growing before he looked up and pinned Elizabeth with a gaze. “You’re right, I’m not,” he said evenly, and some of the tension seemed to leave the room. “Because Radek is a competent and capable Engineer that this city needs. I was making a point.”

“What is that point?” Elizabeth demanded, crossing her arms over her chest.

“That you cannot bully me. You cannot cajole my scientists into doing your dirty work for you,” McKay said. “I will be sending out a city-wide email, reminding people of the security requirements as put forth by the Charter we all signed. It’ll also be good for people to reacquaint themselves with how the city is supposed to run.”

“What does that mean?” Elizabeth asked, and John thought he could hear fear in her voice.

“It means that people have forgotten that you’re not always in charge of what happens in this city,” McKay said evenly. “if the problem is scientific in nature, I assume control of the city while working in tandem with the Military Leader and the Expedition Leader. Neither you nor Colonel Sheppard has the background or experience to make those decisions. It’s the same way that in a Military situation, Colonel Sheppard assumes control of the city because neither of us has the background or experience to make those decisions.”

Silence followed, and John sat up a little bit at that, frowning at the screen. He glanced at Lorne, who didn’t seem surprised by this, and John suddenly felt shame, wondering what he had missed.

“What?” someone else in the room said, and Rodney looked over for a second before back at Elizabeth.

“That means, Dr. Weir, that the next time you try and countermand Colonel Sheppard’s orders regarding a clear military situation, such as, say. Rescuing Sumner or dealing with an infected individual who is interfering with the security of this base. Then you will have to explain to everyone why Colonel Sheppard is backing down on the orders of a Civilian diplomat.”

With that, McKay turned and left, stunned destruction in his wake.

John reached out again and hit the pause button with a frown. “What?” he asked, looking between Lorne and Radek, who were both nodding.

“You didn’t know, sir?” Lorne carefully asked as he walked back to the front of the desk and sat down.

John sat back in his chair and rubbed his face. “Lorne, I signed up for the Expedition a few weeks before it left. I barely had time to get my affairs in order. I signed the Charter and never read it. I assumed Elizabeth was telling the truth when she told me she was in charge and I answered to her,” he admitted with a groan, dropping his head back, feeling like an idiot right then. “Why didn’t anyone tell me?”

Silence followed, and John looked up at Lorne and Radek, who were both looking at him with wide eyes.

“What?”

“You assumed a civilian was in charge of the Military on the base?” Radek asked, tilting his head to the side.

John felt shame settle deep into his gut, and he glanced to the side, slumping back into his chair. “I never expected to be in charge, so I didn’t bother reading it. I wasn’t even in the Chain of Command and assumed Sumner would tell me what I needed to know. I came here to be a light switch, nothing more.”

“The two incidents Dr. McKay mentioned,” Lorne started carefully, spine straight. “Perhaps people didn’t realize you were uninformed.”

“Elizabeth reamed me out for breaking quarantine during the whole thing with Peterson and the nanites back first year,” John explained. “It’s not the first time a CO has reamed me out, so I didn’t think anything of it.”

John was silent, the room silent around him before he sighed, rubbing his hands over his face and feeling the weight of his fuck up suddenly settle onto his shoulders. “I’m an Air Force Officer, not a Marine. I didn’t fit in. I just started giving orders out of habit, and people followed. I didn’t stop to think why. I assumed she didn’t think that the Marines would follow me, which was why she didn’t want me to get Sumner. To be fair, a lot of them didn’t respect me until after the Genii.”

“Elizabeth,” Radek began carefully. “Has many strong qualities, she is stubborn, determined, and she is good at her job, but I feel that her stubbornness and determination are also detrimental because she wants to be in charge and does not like to be shuffled to the side.”

John leaned back, tapping his fingers on the desk. “Maybe, but she had to assume someone would tell me eventually, and then what? Or maybe she assumed I already knew and was following her orders regardless.”

Radek and Lorne both shrugged but glanced at each other.

“It was the second one, wasn’t it?” he asked, wishing he was back in bed sleeping as they both nodded. “Fuck.”

John dropped his head into his hands, wondering if what people had told him time and time again was true. That he had made it to where he was because of family, and not because of how good he was. He never thought he was the greatest commander, but he thought he had been doing good on Atlantis. They had let him keep his command, and he had taken that as encouragement that he was doing the right thing. Except now, he felt like a failure, like some snot-nosed kid who got promoted because he had family connections.

John hated those people, and now he seemed to be one of them.

“What about Rodney?” Radek asked. John glanced up and found himself on the receiving end of an intense gaze.

“What about him?”

Both Radek and Lorne raised their eyebrows, and he fought the urge to cross his arms across his chest. “I am allowed to be mad at him.”

“It’s been four months since Doranda,” Radek scoffed. “I cannot tell if you are more stubborn than him or more stupid than Elizabeth for that.”

“I’m not stupid,” John defended, feeling all of sixteen with the way Radek was looking at him.

“Rodney fucked up. He is the first to admit it and reached out for apologies even though no one made him. He has more than made up for his mistakes, yes? Is a big mistake, but it was a mistake, one done out of goodness, the same way you giving Teyla her necklace back was a good deed with bad consequences,” Radek said patiently. “Perhaps you should figure out why you are still mad at him when those of us that he actually hurt have already forgiven him.”

“He tried to fire you,” John pointed out.

“Bah,” Radek said, waving a hand. “It was not absolute, but I was pretty sure he would not, which is why I emailed Evan. We might not always agree, but Rodney is a good friend of mine, and he has earned my trust, as I have his. Is not such a fleeting thing, not out here.”

“Okay, okay, Jesus,” John muttered, and Radek smiled. “I get the point.”

“Is not a point, Colonel,” Radek said, shrugging. “Is just the fact. Figure out why you’re still so pissed off, and then figure out a way to kiss ass because Rodney is not going to take this lying down. He never does.”

“Never?” John asked.

Radek snorted. “Do you really need to ask me that?”

John thought of Rodney, holding a P90 in inept hands, terrified and wide-eyed but so ready to help capture a Wraith. He thought of Rodney, facing down Koyla despite the torture and lying to him time and time again. Of facing Koyla to protect Elizabeth, of facing him a second time after he had been tortured. Of the thousand times when Rodney stood his ground despite how terrified he was, and he sighed, dropping his face into his hands.

“Fuck, just, fuck me.”

“You’re not my type,” Radek said, standing and leaving without saying anything else.

John looked at the sheaf of papers Rodney had left and pushed the birth certificate away without reading it, not needing that reminder. He pulled the Charter that was underneath it closer to him and looked at the title. ‘The Atlantis Charter as granted by the SGC and IOA.’

John had never been one for introspection, he hated to think about the past, and he knew he didn’t always have the right reactions to things. He slept fine after killing the Genii during the Siege, but trying to talk to someone about how he felt could keep him up for days. But looking at the Charter and hearing the silence as it grew made him realize that he had fucked up and hadn’t even realized it.

He had always thought that he was a decent CO. Maybe not the most inspiring, but his men followed him, they listened to him, and no one had filed any major complaints against him, so he’d assumed he was doing okay. He rubbed a hand over his face and looked at the bottom of the first page, seeing Elizabeth’s tiny and neat signature, right next to Sumner’s tightly written and computer-neat signature. Rodney’s was on the right, barely legible, and the strokes bolder than the other two.

He didn’t want to think about Rodney or think about the situation between the two of them. There was so much John suppressed that he didn’t want to bring it up, not in front of Lorne. There were easier topics to focus on.

“How bad?” he asked softly, looking up at Lorne, who was looking at a point over John’s shoulder, his face blank. John knew that blank look. He used it himself anytime a CO asked him a question he didn’t wasn’t to answer.

“Sir?” Lorne asked, voice inflectionless. It was evident that Lorne didn’t expect much out of him, the man had shouldered most of his work without question, had caught up on John’s backlog, and John had never even questioned it.

“How badly have I fucked up.”

“Sir?” Lorne said again, glancing to John and down at the papers before looking back over his shoulder.

“I like to think that, despite everything, you know I’m not going to rip you a new one if you tell me,” John said, sitting back in his chair and slouching down. “Right?”

“Right, sir.”

“So,” John said, crossing his arms over his chest and letting the silence grow. The silent game was one he did well, and watched Lorne for a few long moments before his XO finally shifted in his seat. He stayed silent, watching Lorne and waiting.

“Sir,” Lorne said finally, sounding pained. “The Marines follow you. That is a testament to your leadership skills.”

“How come?”

“How come what?

“How come they follow me?” John pressed.

Lorne shifted again, glancing to the side. “You’ll always come for them, sir, and they know that. You’ll be standing on the front line, taking the bullet meant for them. You have their back.”

“Is that the only reason?” John pressed, and Lorne stood up quickly.

“Permission to be excused?” he asked, his voice tight.

John sighed. He had his answer. “Granted,” he said, waving a hand.

Lorne looked relieved, and John watched as he moved to leave, stopping when John cleared his throat. “Silence is sometimes louder than words, Major,” he said softly, watching the line of Lorne’s shoulders stiffen. “And discretion is the better part of valor, but it wasn’t needed here.”

Lorne saluted and turned and left, and John let him. The door slid behind him, and he frantically thought lock to Atlantis, needing the room to himself as he went over the past year and a half. John knew what the problem was. He had gotten lazy and hadn’t cared. If he was honest with himself, he hadn’t cared since his team had died back in Afghanistan. He had been going through the motions ever since.

The complete lack of surprise on both Lorne’s and Radek’s faces had thrown him. Clearly, a lot of people thought he was letting Elizabeth call the shots, even though Rodney had been right, and she didn’t have the experience.

“Fuck,” he said, pressing his face into his hands.

He suddenly felt tiny, the failure pressing him down into the chair. He had always felt guilty about not getting to Sumner in time, and now that was magnified with the realization that if he had just taken control, he could have left earlier, and Sumner would maybe be alive.

John had failed Sumner, but he would be damned if he failed anyone else.

He sat up and rolled his shoulders, grabbing the Charter and pulling it towards him, beginning to read it like he should have done before he had signed it. He could hear his Grandpa yelling at him for that, calling him a useless idiot, and right then, he agreed.

John was not going to be some snot-nosed legacy promotion, not anymore. He had been a fantastic pilot and a great team leader, and he was going to earn the right to call himself a good commander.

It had taken him three hours to read the charter. Three hours to do something he should have done a year and a half ago, and he was kicking himself for that now. There were so many instances where he had failed, and it made the guilt sit even heavier on his shoulders. He had fucked up, and it had taken Rodney coming in and yelling at him to realize it. It made him feel like he had been backed up against a wall and forced to see what he had been willfully ignoring.

“Fuck,” he breathed out, scrubbing both hands through his hair as he thought over what he needed to do next. He needed to talk to Elizabeth and figure out what was going on there before he even started trying to think about this thing with Rodney.

There had been times when John had been exhausted from tour, and Nancy would manage to wear him down enough with her demands that he would tell her something innocuous. A story of the moonlight over sands, the way the bazaar smelled in the morning. Little things to get her to back off, and whenever did, Nancy would always get this smile. A smug look of superiority that she was wearing him down, not realizing that all she was doing was pissing him off.

Elizabeth had had the same look on her face when Rodney had left the room, and like Nancy, it had made John’s hackles rise. He watched the video a few more times, paying closer attention to both of them, wanting to get a better read on both of them. Rodney was easy; he had never been good at hiding what he was thinking or feeling. Elizabeth was a diplomat, but John had grown up surrounded by them, and he knew what to look for.

Elizabeth was glad that Rodney was angry and paranoid, and John had no clue what to make of it. He wondered when their relationship had dissolved and realized with a jolt that it was around the same time John had let his relationship with Rodney slide. It was something else he had missed, and he didn’t know how much more of the weight he could handle. For a brief moment, he felt a sense of loss he didn’t have a name for before he pushed it away and focused on the slight smug tilt of Elizabeth’s lips in the paused video.

He closed the file down and took a few moments to get his head on straight. He wanted to do this right, and he knew whatever waves he would start making would only grow, and he needed to be sure he could handle it. His mind flashed to Rodney, yelling at him, and the realization suddenly struck that Rodney hadn’t even looked surprised when John had snapped back. He looked resigned. As if Rodney had been expecting it.

“Fuck,” he muttered again, knowing that repairing his friendship with Rodney was going to be a long battle, but he had to prepare to do it. Rodney was worth it. He had no clue what to expect with Elizabeth.

It was late in the day when he knocked at her door, not surprised to see her still working in her office. He waited until she acknowledged him before stepping in and letting it shut behind him, mentally thinking on to the privacy feature, glad when the windows went opaque, and the feeling of silence dropped down, boxing them in.

“John?” she asked as he took a seat and leaned back, not wanting to start this argument by looming over her.

He let the silence stretch for a moment, trying to figure out how to do this delicately. “I saw the argument between you and McKay,” he said, keeping his voice even, choosing each word carefully.

Elizabeth leaned back, her posture mirroring his. “And?”

“And what the hell,” he demanded, one arm thrown out to the side, any need to tread carefully suddenly gone in a flash of anger. “I agree with you? I didn’t even know you were spying on McKay, and if I had, then I wouldn’t have agreed with you.”

“I meant that you agreed that he needed to be watched,” Elizabeth corrected, attempting to sound reasonable.

John shook his head. “That is not the way he or anyone else in there took it, and you know that.”

Elizabeth shrugged her shoulders, her chin raised slightly, reading herself for the fight. “He needs to be managed,” she said, her voice soothing, and John felt anything but soothed. He felt like he was in divorce proceedings all over again with his ex-wife and his Dad glaring at him. “He was out of line with Doranda.”

“He’s older than both of us,” John said, rubbing the back of his neck, flashing back to the copy of the birth certificate he had locked in his desk, a reminder he wasn’t going to need. “He’s got a dual doctorate, and he’s been working for the SGC longer than both of us. Combined. He earned his position and, personal feelings aside, he is good at his job.”

“He failed,” Elizabeth said, anger cracking her calm facade. “He could have killed you both.”

“I almost got killed my first day because I woke the Wraith,” John replied. “We’re exploring another galaxy. It’s dangerous.”

Elizabeth shook her head. “Rodney needs to learn that he is not infallible and that he has a place on this mission, and it’s not running around doing whatever he wants for the sake of his ego.”

John opened his mouth, but Elizabeth cut him off, eyes narrowing in anger. “You would do well to remember, Colonel Sheppard, that you are here by my grace.”

John’s mouth snapped close with an audible click, his eyes narrowing. Of all of the arguments he had expected, that wasn’t one of them. John had never been backed into the wall and given in gracefully, he would fight tooth and nail until he was free. The more someone would try and push him, the more he would buckle down and argue, never wanting to let someone else get the upper hand. He had been called scrappy as a kid for that reason. He had never backed down from a fight, not even when he was outmatched.

He was silent for a long moment, taking in her posture, her body screaming for him to fight her, and John was ready for that fight. He leaned forward, resting his elbows on his knees and fixing her with a solid stare, letting the moment linger long enough she started to look uncomfortable.

“Dr. Weir,” he finally said, giving her an insincere smile. “You’re correct. After the first year your word let me keep my position, but if you think for one second that I have not earned my Command since then, you are mistaken. I would suggest looking at my jacket and seeing the commendations for my actions from both General O’Neill and General Landry.”

Elizabeth’s smug look wavered, and John smiled a little bit wider. He might be mad at Rodney, but that was a personal matter, and he made sure it didn’t affect their professional relationship. They had worked well in the field together since, and John had made sure of that. It was something Elizabeth needed to remember.

What she needed to learn was that John wasn’t going to back down to her demands so easily, not anymore. He knew his job, and he had fucked it up. He could feel the sense of failure at allowing a civilian to control his Command sit heavily on his shoulders, and he knew it would be an uphill battle to change the way people viewed him. But he was ready to begin.

“I might have gotten into this position through a combination of luck and misfortune,” he said, thinking back to Rodney’s words and knowing they were also right. John had crashed into this job, and he had fallen down on his duties. “And your recommendation might have helped to keep me here, but from the moment I stepped back onto this city with official orders to retain command that changed. Your word is not keeping me in Command, my own actions are. ”

Such as they were, and John wondered what O’Neill and Landry honestly thought of what he had done. He wondered why the fuck he had kept his job. He had so many questions, and Lorne wouldn’t answer them, not yet.

John stood up and looked down at her, taking in the tense line of her shoulders, the angry slash of her mouth. He wondered where this anger, and inability to see what she was doing came from. She had always seemed rational, almost as if emotions were beneath her. And now she seemed to be ruled by them. He could only hope that she would snap out of whatever she was doing soon because he wasn’t going to back down.

He thought about saying something else, but unlike Rodney, he didn’t like starting fights for the sake of arguing. He preferred to bide his time if he was going to, and he knew that Elizabeth needed some time to settle before they talked again. He also needed his own time to cool down. Her dig at his Command was enough to get his blood boiling, and he wanted nothing more than to yell right then.

Except, he knew she had been right. He was here partially because she had wanted him, and he could never thank her enough for it, but he didn’t want to be here by her grace anymore. He wanted this Command because he deserved it.

He nodded his head when she didn’t say anything else, watching him with barely hidden anger. He left before she could say anything else, leaving her stewing in her silence, trying to ignore the trepidation building in his gut.

Two

John made his way to where Teyla and Ronon were at the common area on the south pier. It was the one place on the city where they could see the mainland in the far distance. It was a nice meeting area for friends, furniture added as time went on, and he was glad to see they were alone as he dropped into one of the chairs and slumped down with a groan.

“What’s wrong?” Teyla asked, marking her place in a book she had picked up off-world recently. It had the sociologists in a tizzy, and John swore up and down she was reading it slowly just to keep them frothing at the mouth.

“It’s about to be World War III,” he said, knowing how stubborn Rodney and Elizabeth were and knowing neither of them would back down.

“What’s a World War?” Ronon asked from where he was stretched out on the ground, shirt off and looking unfairly comfortable. John’s back hurt just looking at him.

“When the whole world fights each other,” he said, rubbing the side of his neck.

Both Ronon and Teyla looked at him with wide eyes. “You’ve had more than one of these?”

John grimaced. “Officially, we’ve had two called World Wars. But there’s been a lot of wars over the years, involving a lot of people.”

Ronon grunted and dropped his head back down, shifting to get comfortable. “Earth’s weird.”

John couldn’t disagree and tilted his head back, closing his eyes and letting the sun warm his face. Between the ocean breeze, the warm sun, and the smell of salt, John felt like he was on a beach somewhere in Hawaii, and all he wanted was a fruity drink and a warm body next to his.

“What will cause this third one?” Teyla asked after a few moments of allowing him to relax. For a brief second, John had almost felt the tension leave his shoulders.

“Rodney and Elizabeth,” he said, shifting a bit to get comfortable. “Elizabeth had Radek monitoring Rodney’s work, and it came to a head today. Rodney fired Radek for a few minutes, Elizabeth and Rodney got into an argument, Rodney came and yelled at me, then I went to talk to Elizabeth, and neither of them are going to back down anytime soon.”

“They are just as stubborn as you are,” Teyla said, sounding amused.

John raised his head and glared. “I had nothing to do with that,” he muttered, not disagreeing with the stubbornness, just on the reason for it. “Not between them.”

Teyla just hummed under her breath, and Ronon snorted. John glared at both of them, not wanting to get into that argument just yet. He shifted and unzipped his jacket, wanting to feel more of the late sun. He folded it and pillowed it behind his head, wishing he could take a nap right then. It would feel so good to sink into the darkness and let this fucking day end, warmed with the sun and with his friends who he knew would have his back.

“You’re mad at McKay, same as she is,” Ronon finally said. “For the whole solar system thing.”

“He blew up a solar system!” he said, but after the day’s events, it felt childish even to him. “He almost killed me.”

“I almost killed you the other day,” Ronon said. “When you didn’t duck fast enough. You mad at me?”

Ronon might not speak often, but just like in sparring, he knew how to land a hit. John glowered and looked to the side, not wanting to see the knowing look. He had known, deep down inside, that he was dragging this out past what was a reasonable amount of time.

“No,” he said finally, catching the knowing looks between the two of them, making him feel like a petulant child.

“Why are you mad at him?” Teyla asked, going back to her book as if his problems weren’t enough to warrant her full attention.

John forced himself to think about her question. He had been angry at Rodney’s inability to see what was happening, but as time went on, John had found himself less inclined to let go of that anger. He had been furious, watching as Rodney spiraled down into ego fueled self-destruction on Doranda and tried to drag John with him. He had seen people go down like that many times, and he had been that person more than once. He had a black mark to prove that he could not pull out of a dangerous dive, not if it meant saving at least one person.

“He put us in danger.”

“Wraith exist. Try again,” Ronon said, rolling onto his stomach like some sort of large cat. John scowled at him for good measure.

John bent over and began tugging at his boots’ laces, getting them undone and pulled them off, his socks following. He shoved the socks into the boots and slouched down, wiggling until he got comfortable. John knew he needed to talk to Rodney. He had to explain what had happened and how the day had gone, but he also knew he needed to figure his own problems out first. John wasn’t good at introspection, but he wanted to understand why he was still mad at Rodney. He had no doubt his other two teammates would lead him the right way.

“Because I’m not suicidal and don’t want to die for this mission?” he half-heartedly tried.

“Wraith bomb,” Teyla said, turning a page, not even bothering to glance at him, and he knew he deserved that one. “You are correct. You are not suicidal, but you would die for the mission in the right circumstances if it helps all of us. If you truly had thought staying another minute would have made the device work, you would have taken that risk.”

He closed his eyes and tilted his face to the sun, crossing his legs at the ankle and folding hands across his stomach, allowing his body to settle into the chair so he could think.

His friendship with Rodney had been a surprise. It had seemingly come out of nowhere and was faster than any he had had before. John had always had friends; he had some fantastic friends. Dex, Mitch, and Holland were holes in his heart he would never be able to fill, and the sense of failure would never go away. He still exchanged occasional emails with his best friend from high school, two of his college roommates, and three ex-girlfriends. And one very hidden ex-boyfriend who had spent time in the Navy and understood the need to keep quiet.

He made friends, and while he liked being by himself, there were some people he didn’t mind being around. Rodney was like none of them though, loud, brash and so full of opinions that sometimes John was surprised the man had time to sleep. He was smarter than anyone John had ever met and had a way of digging his heels into the sand so that even the ocean would lose.

“He’s my best friend,” John admittedly, hearing identical noises of agreement, although neither of them pressed for more, just letting him work through this on his own. John didn’t mind being alone; he just found he liked being alone with Rodney better.

He thought back to that day, forcing himself to think back on his feelings during the moment. He could remember the joy Rodney had when they found what the machine on Doranda did, the sadness of losing Collins, and the absolute certainty in Rodney’s voice that John trusted more than his words. Rodney would fix this and fix the mistake he had made in waking the Wraith, and no more people would die. Rodney had failed, he had let his ego control him, and they had almost died for it and had lost a weapon that would have turned the tide of the war.

He let out a long groan. “I wanted him to be able to fix the weapon so badly, so we could end the war with the Wraith, and it could fix the mistake that I made. He was so sure of himself, and I wanted so badly to believe him that it overrode my common sense.”

“If the city was sinking and he came to you with a plan, would you question or would you go with it?” Teyla asked, looking up from her book and pinning him with a stare.

John huffed. “I’d go with it.”

“And if the plan was risky and could fail?”

John knew what the angry part of him wanted to say, but that rage was cooling as he allowed himself to think back on the day. He sighed finally, shaking his head. “I’d still go with it.”

“Because he has earned our trust,” Teyla replied, looking back down at her book.

“Did you wake the Wraith on purpose?” Ronon asked before John could talk.

“No, of course not,” he snapped, tensing back up.

“Actions have consequences,” Ronon said, opening his eyes to look up at John. “Not always good, but you can’t see the future.”

“It’s still my fault,” he said softly, that guilt a tight knot under his breastbone that would never go away. Even if he became the best Commander the city had ever seen, John knew that guilt would never go away. Nor would the guilt for the failures he had made in the past year and a half.

“Yeah,” Ronon said, closing his eyes again. “But you didn’t run, you stayed, and you’re fighting, and you’re going to keep fighting. Makes you brave, not a coward.”

Ronon’s quiet agreement hit him like a physical blow, and he let out a stuttered breath, closing his eyes. He ignored the thud of a foot hitting a body and Ronon’s grunt. He pressed a hand over his face as he thought about Rodney, standing tall while facing off against the Wraith, by his side no matter what was happening. Even during the past few months, Rodney had been by his side, even when John had done everything to run in the opposite direction.

“John,” Teyla said softly, taking his hand and pulling it away from his face. “I took you to the ruins. I took you to that place where you found my necklace. I played a role in this, as well.”

John scoffed and shook his head, keeping his eyes closed. “I shot Sumner,” he said softly, getting to the crux of the matter. “I touched the necklace, he got culled, and I went to save him and had to shoot him. I shot him, and the Wraith woke up.”

Teyla held his hand in both of hers and squeezed. He opened his eyes and looked at her, face serene and intent on his, and she shook her head. “Would you have wanted anything different if your positions were reversed?”

John shook his head. “No.”

“A peaceful death for my people is a luxury few can afford,” she said softly. “But to deny the Wraith even a few years? Now that is worth something. It is a hard lesson we all have to learn, but no one faults you for that.”

John remembered Charin and the Ring ceremony a few months ago. The Athosians refusing the leave Atlantis even as the Trust planted bomb counted down, if only to give Charin a proper goodbye and a peaceful end.

He sighed. “I fault me.”

He was glad when she didn’t say anything. It would all feel like false platitudes right now. The guilt was complex and tied up with so many other emotions. His first day through the gate had been long, complicated, and so much more than anyone had anticipated.

Teyla smiled and stood up, leaning down to press her forehead against his own, and he closed his eyes, taking the comfort for what it was. She pulled away after a few seconds and moved to sit back down, letting him sit in silence. He knew it wouldn’t be too long. Teyla was a hunter, and she always waited for the right moment before attacking.

“Now, about Rodney.”

He sighed. “He’s my best friend. Or I suppose he was my best friend. Now I don’t know.”

“Said that already,” Ronon said from the ground. “Never had one before?”

“I have,” John replied, not offended by Ronon. “I’ve had a few.”

“So why do you sound surprised when you say it about McKay?”

John paused for a second, thinking back to how he had said it, and relaxing that Ronon was right. He did say it oddly like he was constantly surprised by it. That he and Rodney could be friends, best friends even.

“Most of my other friends are like you two,” he said softly. “Military, active people, nothing like Rodney.”

“I don’t think anyone is like McKay,” Ronon muttered.

There was nothing John could say to that, so he just nodded. He didn’t want to tell them that he preferred to be alone with Rodney than be alone by himself, that even Teyla and her calm serenity was too much for him sometimes. He couldn’t explain how Rodney’s constant babbling was more soothing to him than silence.

He wondered if they knew how he felt about Rodney and didn’t know if he wanted them to know. He scrubbed a hand through his hair and forced himself to think back to that day. He was standing in the control room with Rodney as he worked hard to get it running. He could remember how badly he had wanted Rodney to succeed.

“I’m mad at me,” he admitted finally, giving words to something he had never wanted to. “I wanted him to be able to do it so badly that I let him keep pushing even when it was obvious he was losing control. I could have gotten him out sooner but didn’t because I let my fear and hope cloud my judgment.”

John wanted Rodney to be right, and he had let it push him to stay longer. When Rodney had failed, John’s disappointment had bolstered his anger over the Wraith and it twisted into something worse. He had known it was irrational, but it had been easier to face his irritation with Rodney than it had been to look at himself and his reasons.

“So?” Teyla said softly. “You are human, yes? We all have moments like that.”

“I could have made him leave earlier.”

“Does it matter?” Ronon asked, opening his eyes and tilting his head to look at John. “Not like you can fix it now.”

John glowered but didn’t reply, knowing Ronon was right. He sighed and dropped his head back, and closed his eyes, trying to calm himself down. He needed to go and talk to Rodney. He knew that. He needed to fix their friendship and apologize for his part in it before it got worse, and hopefully, that would settle whatever was going on between Elizabeth and Rodney. The three of them needed to present a united front, especially if John was going to be better at his job.

“And what else?” Teyla asked, and John’s eyes snapped open.

“What do you mean what else?” Both Teyla and Ronon turned to look at him, and he dropped his head back with a groan. “You can read more than Wraith minds, can’t you?” he accused Teyla half-heartedly.

She smiled at him and shrugged, turning another page. He wondered if she was reading or not. He sighed, turning his head to watch as the sun started to sink below the horizon, turning everything a purple-blue-red that almost looked normal except there was something alien about it. John couldn’t put into words what was odd about it. Everything about Lantea was so close to Earth, but it was still so alien. The smell was different; the way the ocean sounded was just slightly different. There was just enough to make it different, and John loved it.

When he had stepped onto Atlantis, he could feel the city waking up, and it had felt like a new chance. It felt like he could be someone new here, far away from the expectations of the people who had known him. He thought he could be someone people looked up to and admired, and he had failed. He had loyalty from his men, and he had earned that through his actions, but he didn’t know what else he had to offer.

John had always been an outstanding pilot, he had been an excellent soldier, and then he had been thrown to the bottom of the world and left to rot, forgotten until the USAF needed him again.

Part of the reason he wanted to be better was because of his team. He wanted to be a better fighter to get the look of respect from Ronon. He wanted to talk more, so Teyla smiled at him without any frustration. He didn’t want to hide his intelligence behind a surfer personality and talk to Rodney.

He wanted to get that impressed smile that Rodney gave his scientists from time to time. He wanted all of Rodney’s smiles, and his touch, the way Rodney would come to him first with something exciting. The way his blue eyes seemed to look even bluer when lit by the wormhole. John hadn’t wanted to admit what he felt for Rodney, the love that had been steadily building, and he felt powerless to stop.

He sighed, long and loud and overdramatic, expressing his annoyance. “Do I have to say it?” he asked, looking over at Teyla. “Can I just admit it in my head and be done with it.”

“Do you want to say it to him?” Teyla asked instead.

John shrugged. “No? Yes?”

“Which one?” Ronon asked, standing up finally and grabbing his shirt, pulling it on, and stretching his arms overhead, looking towards the sunset. It was so short on Lantea, the day turning to night almost like someone was flipping the switch. He turned his head and watched, staying silent as the lights began to come up around them and the sun continued to drop beyond the horizon.

“I want to tell him,” he said as darkness began to slide over the pier, taking the last of the warmth with the setting suns. “But I know I need to apologize, and I don’t want him to think it’s a way to make him forgive me. And I’m scared he won’t want to be around me.”

John had met many people in his life that he was interested in, both men and women. Some of the men had responded badly when he had told them he was interested. He had more than one friendship ruined with his confession. He fell for people easily, drawn in because of their brain or their smiles. He liked people. He didn’t fall in love easily, but he fell in like often enough to earn him more than one womanizer reputation.

“You think he would?” Ronon asked.

“I know right now he thinks I’m working with Weir to try and undermine his authority, and I need to get that out of the way first,” he said, feeling anger at the situation again as the cool air of the night began to chill his skin.

For a brief, dramatic moment, he thought about letting the cold seep in but grabbed his jacket and pulled it on instead, bending over to begin to put his shoes and socks on, wanting to somehow trap the warmth from the sun on his skin forever.

“So once that’s out of the way,” Teyla said. She sounded like it was the easiest thing in the world. John admired her optimism. “And you told him, do you think he would respond badly?”

“Respond badly? No,” John said, stuffing his laces into his shoes. “Not want to spend time with me, maybe.”

“Do you think he would?”

John dropped back into the chair, pulling his knees up, feeling like a child sitting like that, but it was just the three of them, and he liked sitting like this, curled up and protected from the world and everything it threw at him.

“I don’t know,” he admitted. “I really don’t.”

“So take it step by step,” Ronon said, dropping down onto another chair, as comfortable in the darkness as he had been in the sunlight. “Can’t do it all at once.”

“So what, apologize first and deal with that, and then tell him I want to drag him into a room with a bed and touch him everywhere?” John asked, a little annoyed at how easy Ronon made it seem.

“Maybe ask him out first,” Teyla suggested with a grin, marking her book and closing it finally, looking out across the ocean.

John could make out the bright yellow that spoke of the night fire from the Athosians’ camp. No doubt the Athosians were sitting around the fire, talking about their day, a family meal at the end of hard work.

“Not everything’s a mountain, Sheppard. Sometimes it’s just a step.”

John frowned at both of them. “Stop being reasonable,” he said half-heartedly. “Maybe I want to be unreasonable about this.”

They both grinned at him, and Teyla waved a hand in the air. “Well then, go ahead, be unreasonable.”

John scowled. “Well, it’s been ruined now, hasn’t it?”

Teyla chuckled and shook her head. “I do not know why you’re making this more complicated than it is.”

“Me either, supposed to be a girl’s job,” Ronon said, pulling his legs out of the way as Teyla kicked him. He stuck his tongue out at her, and it was Teyla’s turn to scowl. For a moment, John grinned at their antics before it faded, wishing Rodney was with them right then.

“I don’t want to make it complicated, and I want to make sure there’s as little fallout as possible in all of this. I need to apologize, that’s step one, and then I need to decide step two.”

“You think he’s going to forgive you right away,” Teyla asked, not taking her eyes away from Ronon, who still had his legs up.

John dropped his head back. “Not in the fucking slightest.”

“So stop planning for step two and see how step one goes first,” Ronon suggested, dropping his legs down carefully only to yank them back up as Teyla aimed another kick.

“She’s not going to stop, you know,” John pointed out. “Might as well accept it.”

“I’ll accept it when you accept that McKay is going to make it hard to get close to him again. You hurt him more than anyone else because he’s your best friend, and you’ve been acting like a dick,” Ronon said but put his legs down, accepting the kick with only a little grunt.

Teyla settled back, looking more settled. “Ronon is right. Rodney will be mad, and angry and you need to prepare yourself for that. And you need to understand where he is coming from.”

John nodded his head. He knew precisely what Teyla meant. “I need to go bribe Radek for coffee and chocolate.”

“Miko’s got Earth potato chips,” Ronon said. “I think she’s got the last few packets on the city.”

“Know what she wants in trade? She doesn’t need me to turn on things like Radek does,” John pointed out. It was his best trade item with scientists—an hour of his undivided attention and time barring emergencies.

“She’s sweet on Parrish,” Ronon offered. “Could ask Lorne about him.”

“I’m not pimping out my XO’s team for potato chips,” John said, even though he thought about it for a second. Maybe a little bit longer than a second.

“Perhaps ask her what she wants then,” Teyla suggested, standing up and picking up her things. “I am sure you can come to an arrangement.”

John didn’t want to uncurl himself from his seat, from the comfortable darkness he was in with his friends, but he knew he needed to. He needed to get dinner, shower, check-in with Chuck, check-in with Lorne, and at some point, figure out what the hell he was going to do with Rodney.

He dropped his legs with a groan and stood up, stretching his arms overhead for a second before dropping them down, shoving his hands in his pocket, waiting for Teyla and Ronon before heading inside with them.

John looked at the packet of chips Miko had just shoved into his hands, trying to make sense of the action.

It had been three hours since he had cleared the infirmary after getting back to Atlantis with Lorne and his team, all of them thankfully alive. The debrief had been somber, helping the Genii plan a coup hadn’t been their intention, even if it had gotten them Lorne, Parrish and the rest of his team back.

John wasn’t upset that Cowen was dead. Cowen had a lack of respect for life that John didn’t understand. There had been nothing but greed in Cowen’s eyes each time they met. John could understand how desperation had driven them to try and lay siege to get medical supplies and C4, but asking for jumpers was greedy, and John had lost any respect for the man. Cowen dying was a good thing, but John still felt dirty for his part in it.

Even though the meeting had been somber, the relief everyone felt at getting Lorne and his team back was obvious. Parrish and Lorne had been a significant part of the city and had been friends with a lot of different people. Even Dr. Rael and Lt. Dale, the other two members of Lorne’s team, were missed in the time everyone thought they had died.

But even with the relief, no one had missed the tension between Elizabeth and Rodney.

John needed to bury the hatchet with Rodney before they buried the hatchet in the each other.

He showered and had barely changed into sweats before his door had rung. Pulling on a shirt, he went to the door, hoping it was Rodney, but instead, he had Miko shoving the chips into his hands with tears in her eyes.

“I don’t have the books,” he said a little inanely, looking up at her, trying to give it back. She had wanted a set of books he knew one of his marines had and was in the middle of reading. He had gotten a deal out of the man to get them after he finished them, jumping the line, in exchange for part of John’s weight allotment on the next Daedalus run.

Miko nodded and folded his hands around the bag. “But you brought David back.” Her hands were tiny and cold, and they were shaking a little bit. He wondered if there was more to it than just her being sweet on Parrish. “You can get me the books when he’s done, but you can have this now.”

John nodded, seeing the determined glint in her eyes, and he didn’t want to fight her on it. “Okay,” he said, managing a smile. “Thank you.”

Miko nodded her head and left without saying anything else, leaving John standing there with a bag of plain old fashioned potato chips and the realization he needed to have a conversation with Rodney sooner than he had anticipated. It had been two weeks since Rodney had yelled at him and had opened his eyes. He thought he would have more time to gather his courage to talk to Rodney. He knew he was dragging his feet, and he needed to fix it. Some part of him wanted to open the chips and eat them himself, but he knew he needed to get his head out of his ass.

He was glad Miko had gotten Parrish back. John needed to figure out a way to get Rodney to trust him again.

He sighed and set the chips down on the table, grabbing an old Air Force sweater and pulling it on, reveling in soft, warm fabric for a second before he shoved his feet into shoes. He grabbed the bag of chips, as well as a small bag of coffee beans he had traded one of the engineers two hours of his time for. Coffee and salt should be a winning combination and a little bit more unusual than coffee and chocolate.

Praying that Rodney wasn’t in his lab, he made his way to the scientist’s room, ringing the bell and waiting. He was glad when he didn’t have to wait long, and Rodney opened the door, dressed in an old worn sweater with a ripped collar and flannel pants. He looked warm and comfortable, and John had to fight back the urge to hug him.

“Colonel,” Rodney said, eyeing him suspiciously, his tone wary. “What do you want?”

“Can I come in?” he asked, wanting nothing less than to do this in the hallway.

Rodney eyed him and his food for a second longer before grunting his agreement and stepping to the side, letting him in. “If this is some half-assed bribe to give in to whatever you and Weir have planned, it won’t work.”

“No, just no,” John said, handing the two bags who Rodney, who only took them after he raised an expectant eyebrow. “It’s the start of an apology.”

Rodney took the two bags but eyed John warily, his eyes sharp and shoulders tense. “Why?”

John pushed his hands into the pocket of his hoodie so Rodney wouldn’t see them fidget. “Because I was a dick, and you didn’t deserve that. I was pissed off, and I think I had the right to be at the start. But what I didn’t have the right to do was make you feel like you needed to earn my trust again. And I am sorry for that. I always trusted you, and I always had faith in you. I was lashing out, and that’s why I said those things.”

Rodney’s eyes were narrowing at him, and John wondered if he was doing this wrong, but he kept speaking before Rodney could start, needing to get this all out before he chickened out.

“I am also sorry for dragging it out. I don’t have any excuse for that,” John said, not wanting to get into why he had dragged it out. There was no way in hell he wanted to bring up his reasoning for that. “I should have gotten over myself earlier.”

John fell silent, wanting Rodney to talk before he did. He wasn’t sure if what he had said was enough, and he needed Rodney to reply before moving to the next step, whatever that was.

Rodney set the bag of chips and coffee down on his desk before turning around and crossing his arms over his chest. “You were an asshole.”

“I was. I am.”

Rodney’s chin raised, stubborn and determined, and John settled in for whatever Rodney would throw at him.

“Why? It’s more than your trust in me. It had to be.”

John didn’t want to talk about it, which meant that Rodney would absolutely make him do it.

John thought about what he had said to Teyla and Ronon over a week ago, and how easy it had been to say it to them, and how hard it felt now to get the same words out. He opened his mouth and closed it again, trying not to fidget as Rodney stared at him, slightly impatient and waiting.

“I was mad at me,” he started before Rodney got too impatient and kicked him out. “I wanted Doranda to work just as much as you did, maybe more because of my part in waking the Wraith. I could see that it wasn’t working and you were losing control, and I let you continue. I let it continue longer than I should have because I wanted it to work. I put both of us in danger because I was scared for it to fail.”

It was so much easier talking to Teyla and Ronon, who never looked at him, instead of talking to Rodney, pinned under those piercing blue eyes.

“If I recall,” Rodney said softly, “I argued against you when you tried to make me shut it down, and I argued when you tried to make me leave. What makes you think trying to make me leave earlier would have worked?”

John shrugged. “You ‑ argue with me all the time, but when I give an order in the field, you always follow it. And this time was no different. When I finally told you to shut it down, you did, and when we needed to leave, you didn’t fight me. I know exactly how capable you are of digging your heels in when you want to.” John dropped his head down and chewed his bottom lip for a second. “That’s why I was mad. I was mad at you, yes, but I was also mad at me, and it was easier to be mad at you than to think about why I was mad.” John raised his head to narrowed eyes and shrugged. “It was shitty, and I’m sorry.”

He fell silent, not sure what else he could say, and watched Rodney, who managed to look both pissed off and happy, something that was uniquely Rodney.

“That’s shitty?” Rodney asked, voice emotionless.

“Yes.”

It was beyond shitty, and John knew it. It had taken Rodney yelling at him about something else to make him get his act together. Rodney leaned against the desk and crossed his arms, somehow looking more imposing like that when he was standing.

“Seriously Sheppard?” Rodney muttered. “You were mad at yourself, so you took it out on me.”

“That about sums it up,” John said, his hands squeezing each other in the pocket of his hoodie to keep himself from fidgeting anymore. “I know it’s shitty, and there’s nothing I can say to make it better. I’m sorry, and I’m going to do better.”

“What if I don’t accept your apology?” Rodney challenged, eyes narrowed, and cheeks flushed with what John assumed was anger.

“You don’t have to,” John said. “I mean, I’d like it if you did, but you don’t have to.”

John didn’t have many memories of his Grandmother, but one of the few lessons she had drilled into his head was that apologies weren’t required to be accepted, and he had to accept that.

“What if I do? What then? We’re fine until the next time I fuck up, and then that’s it?” Rodney demanded.

“Well, Teyla might smack me if I did it again,” John said, trying to get some levity into the situation and watching as it fell flat. He sighed and looked to the side, feeling pinned under the blue gaze and feeling unnerved by the stillness. “I won’t.”

He looked back at Rodney and shrugged. “I won’t do it again.”

Rodney scoffed. “I don’t know if I trust you. You might have to earn it back.”

John flinched. He knew he had deserved that. He stayed silent, knowing nothing he would say would make up for it, and Rodney sighed, rubbing his forehead.

“What do you want out of all of this?” Rodney asked, sounding tired.

“I want my friend back,” John said honestly. Friendship was a good step. He could deal with emotions and relationships later.

“Are you just doing this because of Weir?” Rodney demanded, leaning forward. “I’m not going to—”

“—Jesus Rodney,” John interrupted before he could get a head of steam going, “There’s no plan between me and Weir. I didn’t even know what she was doing until you came and yelled at me. And if I had, I would have told her to back off. Any issue you and I have with each other is personal, not professional.”

Rodney seemed to settle back, his arms seeming to tighten around himself. “What she did was unacceptable.”

John nodded. “It was. Even if she felt like you needed to be supervised, which you don’t, asking someone to spy on you was out of line. That’s not how things work.”

The silence stretched between them, and John didn’t want to break it because he was afraid Rodney would take his words the wrong way.

“I’m pissed off,” Rodney said finally. “I’m pissed off, and I’m hurt, and I’m going to be hurt for a little bit longer. But I accept your apology.”

John had assumed he would feel relief if Rodney ever forgave him, but he was surprised at the weight that seemed to lift. “I’d be surprised if you weren’t,” he said honestly, pulling his hands out of his hoodie pocket, only to shove them into his pants pocket, forcing himself to relax.

Rodney nodded, a hand rubbing the side of his neck before he jerked his head towards the small table. “Chess?” he asked.

John blinked in surprise, and he opened his mouth for a second before closing it, tilting his head in confusion at Rodney. Rodney shrugged again, walking over and sitting down at the table.

“Only way is forward, Sheppard, and that takes time and action. You want to be my friend and want to bury the hatchet between us, well, that means we need to sit and talk to each other. So, might as well start now,” Rodney said, pulling out the small chessboard they used and began to set it up. “I also don’t think I can sleep anytime soon. I’m still keyed up from today.”

John blinked in surprise as he watched Rodney set up the game with quick motions. He quickly walked over and sat down, not wanting to give Rodney a chance to change his mind. He forced himself to relax, leaning back in the chair, not wanting to crowd Rodney. He watched Rodney for a moment before he cleared his throat, waiting for Rodney to look at him.

“I know what you mean,” he said softly. “Thank you.”

Rodney shrugged his shoulders, his hands fiddling with the chess pieces in front of him. “It’ll be good to have a challenge again.”

“Can’t find anyone to beat?” John asked, wanting to be careful. This thing between them felt fragile and new, like a spider web, ready to be blown away at any moment.

“No,” Rodney said. “It’s too easy.”

John smiled softly, knowing the compliment in there, hidden as it was. “My Grandad taught me how to play,” John offered. “As a kid. He was a Grandmaster. I remember every single game I won against him.”

Rodney hummed and set down the final piece before reaching out to make the first move, sliding his pawn out. John didn’t think before putting his knight into play, loving the unpredictability of it. He leaned forward, resting his elbows on his knees and clasping his hands together out of sight, trying not to twist them together until they ached, a bad habit that he had never been able to break.

“I wanted to become one,” Rodney said, looking at the board, already too intent for the second move, but John had come to expect that. “But I didn’t have the time, and I thought it was too easy as a kid, not realizing I wasn’t facing people who could challenge me yet.”

John nodded, moving a piece after Rodney had moved his, enjoying the slight glare. John’s tendency to move without thinking and trust his instinct had annoyed many people over the years. Rodney was no different than most people he played again, looking at the board and all the options before making his move. It worked for most people, but John easily got lost in the what-ifs if he did that, and the game would drag out and not in a good way. He needed to move without thinking, trusting his gut because his brain got him into trouble. They were silent for the next couple of moves, capturing pieces back and forth a few times, before John sat back, fingers fiddling with a pawn Rodney had taken.

“Why didn’t you ask more about Elizabeth?” John asked, watching as Rodney’s hand hovered over the board.

“You don’t lie,” Rodney said, fingers gripping the top of his knight before pulling his hand back to rap his fingers on the edge of the table.

“Yes, I do.”

Rodney shook his head, glancing up at him before looking back down at the board. “Everyone lies. It’s called being human. But, you’re not a liar. And there’s a distinction there.”

Rodney’s hand reached out and moved his rook finally. John glanced at the board and moved his knight before looking back at Rodney, who grimaced. “What’s the distinction?”

“Trust,” Rodney said, moving his bishop faster than John had expected him to. It took him a bit by surprise, and he frowned at the board, wondering what he was missing, what Rodney saw that he was missing. John chewed his bottom lip and reached out, finally moving his knight again, falling back on the moves he knew well.

“Thought you didn’t trust me,” John said softly, feeling the ache in his chest at the thought. He wondered how the fuck Rodney hadn’t punched him in the transporter when he had thrown that line in his face.

“I said I don’t know if I did, not that I didn’t,” Rodney explained, moving his pawn again quickly. John shifted and kept his eyes on the board, moving his rook and capturing the pawn Rodney had moved. “I think you’re a good person, and so I’m trusting you at your word on a professional level. You say you’re not working with Elizabeth to undermine me, then I believe you for the moment.”

Rodney captured his bishop a second later, and John frowned, still feeling like he was missing something. “And personally?”

“Personally,” Rodney said with a sigh, crossing his arms over his chest. He was silent for a long moment, eyes on the board before looking up at John and pinning him with his gaze. “Personally, I’m hurt and angry, but I want my friend back as well. So it goes back to trust. I’m trusting you that you didn’t lie to me, and I’m trusting you that you want to be my friend back, and I’m using that trust to start moving forward.”

“You think there are different types of trust?” John asked, ignoring the game for a second and looking up at Rodney, taking in the wary posture and the look of hope in his eyes. Their friendship had always been easy, and it had made John worry that he would have to work for it.

“I trust the cooks to make me something I can eat. I trust Carson to keep me healthy. I trust the marines to have my back,” Rodney said. “Doesn’t mean I trust them with my deepest darkest secrets.”

“Fair,” John said, moving his rook, leaning back and mirroring Rodney’s posture. It hurt more than he thought to be placed in the same category as those people, but there was nothing to say to it.

“I trust you,” he said, chewing on the inside of his lip. “I don’t think I said that before, or if I implied it, but it needs to be said. I do trust you, personally and professionally.”

Rodney leaned forward, looking at the board for a long moment before moving his pawn, fingers resting for a long moment before he let go. “I’ll get there, personally, as long as you meant what you said.”

John nodded his head. “I want to be better,” he admitted softly, reaching out to fiddle with a piece again.

He kept his eyes on the board, not wanting to look at Rodney right then. He was trying to make sense of the game and what Rodney had said.

“You apologized,” Rodney said. “That’s being better.”

John shook his head. “No, not just with this, with us. When you came and yelled at me, I realized that I had been letting a lot of things happen that I shouldn’t have, and everyone deserves me to be better.”

“You’re doing fine. No one wants to overthrow you as the military leader,” Rodney said, waving a hand. “And the scientists like you.”

John managed a half-smile at that, knowing the compliment for what it was. “I was never meant to be in command, and I want to be someone they can look up to instead of someone they know will take a bullet for them.”

“Isn’t that the same thing?” Rodney asked.

“No, anyone can take a bullet. I want to be a Commander that is worth their respect, and I’m going to start being one now.”

“So is apologizing to me part of it?” Rodney asked slowly, eyeing him warily.

John looked up and shook his head, meeting Rodney’s gaze. “I apologized to you because I wanted to, because you’re my best friend and because you deserved one.”

The smile John got was the first real smile he had gotten from Rodney in a few months, and he smiled back. He had been mad at himself and had lashed out at Rodney, and in doing so had shaken Rodney’s faith in him as a friend. John wasn’t the only creator of the problem, but he was the one that had held onto his anger longer than he should have. He had to accept that and prove his intentions to Rodney. It terrified him, but John wanted to know if there was something building between them, or if it was only him.

It hurt to think about it, but he could only do his best to move on from the weird limbo they were in. John smiled suddenly, seeing what Rodney had been doing, and reached out, moving his knight again, capturing the pawn.

“Draw.”

Rodney looked at the board for a long moment before he smiled and leaned back, nodding his head. ”I guess so.”

John looked up at Rodney, who looked back at him evenly, and he nodded his head. “Again?” he asked, waiting for the nod before he began to reset the board. Once John finished, he turned the board, taking white and making his first move.

Three

“I don’t like it.”

Rodney’s voice broke the silence that had fallen after Carson had finished his explanation about the retrovirus he had created. John turned and looked at him with a frown, wondering what had bothered Rodney enough to make him speak up.

“Why not?” Carson asked, looking a little annoyed. Elizabeth looked pissed off, which was becoming more and more common every time she looked at Rodney.

“It seems reckless,” Rodney said, leaning forward and tapping at something on his tablet. “I understand how the Ancients made the Wraith, but that was thousands of years ago. We know there are a few Wraith that old, but we can assume most of the Wraith aren’t. The DNA isn’t technically artificial anymore, not even taking genetic drift into account. So, how can you assure us that stripping the Iratus DNA out of the Wraith will not end up creating something like the Colonel? Strong, driven by instinct and hard to control?”

John was glad that his memories of that time were disjointed, flashes of strong emotions more than memories. It made it easier to forget that he turned into a bug, and he didn’t have to think about it unless someone brought it up.

Carson nodded. “Rodney, what happened with the Colonel was different than what I’m proposing with this retrovirus. He was a human with leftover Iratus DNA, and when Elia attacked him that leftover DNA was amplified due to the way the retrovirus reacted to Elia. I didn’t realize the bloody queens were genetically different than the males. Thankfully, this retrovirus is for the male Wraith, and instead of amplifying, it’ll strip it.”

“Okay,” Rodney said, frowning but nodding his head. “By removing the Iratus DNA, you are left only with the human DNA. How much human DNA is there left? What parts of him are human? How does that affect organs, aging? We know they can eat but get nothing from it from a nutritional point of view. Without the Iratus DNA, will this Wraith be able to eat, or will he starve to death?”

Carson shrugged. “The problem is we don’t know, and unfortunately, we won’t know until we run the experiment. There’s so much about the Wraith that we dunnae understand, and none of them will sit down and talk to us.”

“Do you have the knowledge to be asking those questions, Dr. McKay?” Elizabeth said suddenly, voice hard and cold. John winced, and he saw Rodney stiffen out of the corner of his eye.

Rodney’s face was blank as he looked at Elizabeth, raising his chin stubbornly. John wished he could find the words to stop this argument, but in the two weeks since he had apologized to Rodney, he hadn’t made any headway, and any discussion about it had both of them shutting down on him, and the topic changed.

“Dr. Weir,” Rodney said, folding his hands in front of him and pinning her with a gaze. “I might not have a Ph.D. in biology, nor a medical degree, but I do have a bachelor’s in biology and a minor in chemistry. I also read the paper Carson gave us and the relevant documentation he supplied, so I know what’s happening. I know what I’m asking, and they’re relevant questions.”

Rodney looked over to Carson at that last bit, and Carson nodded after a second. “They are,” he admitted, although John could see the reluctance, and he wondered if it was because he didn’t want to get in the middle or because he didn’t want them asked.

Rodney paused to let that sink in, and Elizabeth’s face turned white with anger, and John could feel the tension rise in the room even more. For a second, John thought that would be that, but Rodney smiled at Elizabeth and tilted his head to the side slightly.

“Do you have any experience in the biological sciences, Dr. Weir?” Rodney asked, pleasantly, a verbal slap from the man.

Elizabeth sat up a little straighter, face pinched. “No.”

“Then it’s a good thing I’m asking these questions, isn’t it?” Rodney continued, blue eyes intense and demanding. “So we know the full extent of what Carson is proposing.”

John rubbed a hand over his face, wanting to sink under the table so he wouldn’t have to deal with the two of them. He and Rodney had been working their way towards something less adversarial since he had apologized a week ago, but it was a ways off from what it had been. Rodney was still holding back, not relaxing like John had been hoping for.

“I guess so,” Elizabeth said, giving him an insincere smile, a hand raising to wave Rodney to continue.

John wondered if he should be keeping score, but he was too afraid to see who was winning at any time.

Rodney watched Elizabeth for another moment before turning back to Carson, who was looking stressed and annoyed at the interruption.

“So, assume we let the experiment continue,” Rodney said, folding his hands together. “What exactly are you hoping for, best case scenario?”

“The Wraith will turn human.”

“Worse case?” Rodney asked.

“They’ll die.”

“Does it matter?” Elizabeth interrupted again, looking frustrated. “What’s the point of all of these questions?”

“This is a meeting to discuss if Dr. Beckett is going to go forward, so questions are important, so we’re all on the same page,” Rodney said, looking back at Elizabeth. “I thought we were all making sure to follow proper scientific procedure now. Or was the reason you yelled at me about something else?”

Elizabeth flushed and leaned forward. “This experiment has the backing of the IOA, as well as my personal recommendation. This is a medical experiment, not science, so you don’t have a say.”

Carson winced at that and dropped back into the chair, rubbing a hand over his face. John wondered what he had missed.

Rodney matched her and leaned forward as well. “All scientific experiments fall under my jurisdiction as the Chief Science Officer, as per the Charter,” he said. “And as per the Charter, there will be no medical experimentation on sapient life, no matter what the sapient life is.”

“The Wraith—”

“—The Wraith are sapient Dr. Weir. Not a single person can dispute that,” Rodney said, looking around the table looking for someone to disagree. No one did. “What we are proposing is to go against the Charter, as well as our own better judgment, to experiment on another species of Sapient humanoid creatures.”

Rodney sighed for a brief second John could see the exhaustion on his face before it was gone in a flash. “But we all agree this has to be an option because xenocide is a lot harder to swallow. But, what I find interesting is no one mentioning other problems that might arise.”

“Which are?” Elizabeth demanded.

“Say it works, say it’s a magical fairy wish, and all the Wraith get turned human. What then?” Rodney asked, looking around. “Do we suddenly drop a couple hundred thousand humans on a planet and say have fun? Do they know how to grow food? Survive in winter? Do we let them keep their ships? Do we think that the Wraith will be thankful for us, or will we suddenly change the war from Wraith vs. Human to Human vs. human?”

Rodney looked around the room as he spoke. “What about the population? The Wraith are predominately males with a few queens. I doubt their reproduction is the same as ours, so how will they know how to care for a human child? What about the native populations of Pegasus? Will they suddenly be okay with the people who ate their friends and family? Will they help, or will they kill any Wraith that comes close?”

Rodney turned to look back at Elizabeth, his eyes narrowing. “I find it telling that you’ve excluded Teyla and Ronon from this meeting, Dr. Weir. Why aren’t they here?”

“They don’t have the knowledge—”

“—neither do you,” Rodney hissed, finally sounding angry. “Neither does Colonel Sheppard, neither does Major Lorne, neither does Dr. Zelenka, and let’s be real, Dr. Weir, this level of genetic manipulation is beyond my experience, so I suppose you were right. I don’t have the experience. So try again, why aren’t Teyla and Ronon here?”

Elizabeth met Rodney’s eyes for a long moment before she broke away, looking to the side. “This has nothing to do with them.”

John winced, and he could see everyone else shifting around, uncomfortable with the idea. Ronon and Teyla were natives to Pegasus, and they deserved to be in the meeting. He felt ashamed he hadn’t noticed it and that they had been left out.

“So, you’re going to what? Fix the Wraith, and then dump them on the native populations of Pegasus to deal with? Is that it?” Rodney asked.

“You’re getting ahead of yourself,” Carson said, trying to diffuse the growing tension. “We dunnae know if this works. It’s counting our chickens before they hatch.”

Rodney didn’t look away from Elizabeth for a long moment before he looked at Carson and nodded. “Yes, but no one has bothered to ask these questions. They’re relevant because if we continue forward, those are things we need to keep in mind.”

“What other option do we have?”

“The same thing we’ve been doing,” Rodney replied evenly. “Kill them, all of them.”

The room went silent after that, and John felt his shoulders tighten.

“That’s xenocide,” Elizabeth snapped, standing up and slamming her hands on the table.

“And what the fuck do you think changing them is?” Rodney demanded, not standing up, but his whole body tensing to fight. John wanted to reach out and grab his elbow to keep him seated, but he was too far away, and this new thing between them was too fragile.

“Do you think the Wraith will thank you? That they’ll look at us removing a good portion of what made them Wraith and thank us?” Rodney demanded. “Do you think they’ll lay down their weapons and give in, or do you think they’ll fight back? And we’ll have opened the door to biological warfare, so who knows what they’ll do next. We saw what they did to Teyla’s people thousands of years ago. We know they’ve experimented on humans before. Maybe they’ll try and change us into Wraith this time?”

John felt cold at the realizations, and he glanced between Carson, who seemed to be white with shock, and Elizabeth, who was getting madder each second.

“As I said, Dr. McKay,” Elizabeth said through gritted teeth. “The IOA, Dr. Beckett, and myself are all in favor of this.”

“Well, I’m not,” Rodney said, standing up and meeting Elizabeth’s eyes without flinching before turning towards Carson. “I am sorry, Carson, your work was well thought out, and I appreciate it, but I’m going to recommend this not go forward.”

“Dr. McKay,” Weir snapped. “This is happening; there is nothing you can do to stop it.”

Rodney pressed his hands on the table and leaned forward, eyes narrowed. “I know,” he said simply. “This meeting was nothing more than courtesy, but my objections are now officially part of the record.”

Rodney stood back up and broke Elizabeth’s gaze, and grabbed his laptop before nodding around the room. “Zelenka, we’ve got work to do. Let’s go.”

John watched as Zelenka nodded and stood up, grabbing his laptop and following. John thought it should have felt like a retreat by Rodney. But it didn’t. He fought against the urge to slouch down as the doors slid shut behind them. He rolled his shoulders as he rubbed a thumb over his jaw, thinking about what Rodney had said. He glanced at Carson, who was still a little pale but not looking deterred in the slightest and then to Elizabeth, who looked like she was going to vibrate right out of her skin as she sat back down.

“Colonel Sheppard,” she said finally, looking over at him. “What are your thoughts.”

“He made some good points,” John said softly, still rubbing over his jaw. “If it does work, it won’t end the war. It’ll just change it.”

Elizabeth shook her head. “He is a pessimist like always. Looking at the bad and never seeing the good.”

“What is the good?” John asked.

“They won’t feed. They won’t need to kill.”

John snorted. “Elizabeth, Wraith don’t kill unless they’re feeding or they’re threatened. They destroyed the Hoffans because they were a threat to the Wraith’s lives, not for eating. Same with Sateda. Rodney is right. They’ll still be Wraith. There’ll still be a war. And they’ll still have the upper hand with the number of ships they have. Sure they might be able to die easier, but they can still bomb our shield until it fails.”

“That’s a pessimistic point of view,” Elizabeth said, looking disappointed in him.

For a moment, John felt the same about her refusal to see anything other than Carson’s point of view. He wondered what happened when she had changed from someone open to different ideas into this. Whatever Rodney didn’t want, Elizabeth wanted, and nothing could deter her.

“If they don’t need to feed, then we can negotiate a ceasefire,” Elizabeth said with the placating smile that always pissed John off, even when they had been getting along.

He shrugged and looked to Lorne, who was looking at his tablet, his mouth in a tight line. Carson still looked deep in thought. “Maybe, if they’re inclined to forgiveness for the bioweapon we use on them.”

“We will cross that bridge when we get there,” Elizabeth said, hands folded in front of her, looking calmer now that Rodney was out of the room. “For the moment, we need to proceed with this experiment so we can take the next steps if it works.”

“Why aren’t Teyla and Ronon here? Teyla, especially in her capacity as a leader. Ronon has experience with the Wraith in ways that we don’t,” John asked, needing to know. Rodney was right. The Wraith had shaped their worlds in a way that none of them would genuinely understand, and it had been a part of their reality for a lot longer than Atlantis had been. “If we’re to proceed with the next steps, then they’ll be useful.”

Elizabeth didn’t look as mad as she had with Rodney, but John could see the tightening around her eyes, and he just smiled calmly, hooking an arm over the back of his chair and relaxing, trying to look less combative than Rodney. John knew how to play the game, a lot better than Rodney did. Then again, whenever Rodney was between a rock and a hard place, he turned into the rock and forced the hard place back. John didn’t even know if he knew the meaning of gracefully giving in, not when he believed in something.

“The IOA felt they would not be able to contribute to this part of the process,” Elizabeth said, looking to the side, her cheeks a little bit redder than they had been.

“Uh-huh,” John said, raising both eyebrows at that. “Because?”

Elizabeth shrugged. “Because their ways are not ours.”

“Their ways are not ours in their home galaxy?” John asked, forcing himself to relax and not lean forward even as he felt anger settle in his gut. “I thought this was your city Elizabeth?”

Elizabeth glanced at him, and he could see the shame for one brief moment before she hid it behind a blank mask. “It is.”

“And I thought Teyla was your friend?”

Elizabeth nodded, mouth pursed in a thin line. “She is.”

John didn’t say anything, and he didn’t need to. Elizabeth knew it as well as he did.

“Why?” Carson asked, sounding as curious as John was.

“Because if a native of the Pegasus galaxy has issues with this plan, well,” John said, looking at Carson. “Better to ask forgiveness than permission, especially if the permission isn’t given.”

“You would think they’d want us to do this,” Elizabeth said.

“It’s not our families that will die if this fails,” John pointed out. “Earth is a long way away. It’s easy to play God when you don’t have a stake in the game.”

“Atlantis could be attacked.”

“We have a shield. And we can retreat to Earth if it fails, where do they go?” John asked before he shrugged his shoulders. “This whole thing is scientific, and so I cannot stop you, but I agree with Dr. McKay.”

John moved to stand, Lorne a second after him, and he picked up his papers. “However, I will not authorize the military to capture a Wraith to bring it to the city.”

Elizabeth stood up quickly, eyes angry. “Colonel Sheppard!”

“No,” John said, looking up, a touch of steel in his voice. “I will not endanger my men capturing a Wraith, and you do not have the authority to make me do so.”

“I am in command of this city, and you will!” Elizabeth snapped.

“You are in command of day-to-day operations, Elizabeth,” John said gently, making his first stand. “As soon as we step through the gate, it’s military. Capturing a Wraith is military.”

“You are under orders,” Elizabeth tried again.

“You are not my commanding officer. If you wish for me to send my men to capture a Wraith, then I’ll need to receive an overriding order from General O’Neill.”

“You mean General Landry,” Elizabeth said.

John shook his head and headed for the door, Lorne a step behind him. “The Atlantis Expedition is under the auspices of the IOA, which means that my superior officer as a member of the American Military is General O’Neill of Homeworld Command. I’ll need the order to come from him.”

John dropped down into the chair in his office, folding his arms in front of him as Lorne sat down across from him. “You think I’ve made a mistake?”

Lorne was silent for a long time, eyeing him warily, and John let him stew. He hadn’t meant to throw his lot in with Rodney so early. He wanted to bridge the gap between the two of them to come to a working relationship again. But what Rodney had said made sense, the points sensible, and John was not going to bring a Wraith onto the city.

“No,” Lorne said finally, still eyeing him. “Dr. McKay made some good points, ones I hadn’t considered. There were a lot of what-ifs about it all that we can’t account for, but I think they needed to be mentioned. That’s not to say Carson’s plan isn’t a good one. I want to know more. ”

“I don’t want there to be more who end up as I did,” John said, remembering that particular point very well. “The Wraith are bad enough, but if we end up with pissed off super soldiers, that’s not going to be good. I don’t remember much, but I know the damage I did.”

Lorne nodded. “He had a point about the logistics if Carson’s plan did work. It’s getting ahead of ourselves, but they’re still valid points.”

“How many on a hive? Couple thousand? Couple hundred hives? There’s not enough food to go around,” John said softly. “The majority of the populations here are small, ten thousand at most, and even that’s rare.”

Lorne nodded and finally relaxed back into his chair. “Their society isn’t set up for it. They’ve never had to grow food, they don’t have the skills to do so, and they’ve been technologically superior for over ten thousand years. And they could still be immortal. We just don’t know. ”

John didn’t want to think about it. The logistics of dealing with suddenly human Wraith sounded like a nightmare. He knew the IOA was going to go forward with it, objections or no objections. Like Rodney had said, turning them human was more palatable than killing them.

“I’m not always going to side with him,” John said after a few moments, rubbing the side of his neck, feeling antsy, like something terrible was going to happen. He looked out his window, watching as one of Atlantis’s moon’s started to sink in front of the sun, blocking the bottom half and casting odd shadows. “Just like I won’t always side with Elizabeth from now on.”

Lorne tensed up again, and John looked over at him, keeping his face blank as he braced his elbows on the desk as he thought about what he was going to say. “I’m going to start taking back some of the duties I’ve foisted off onto you,” he said finally. “You’re second in command of Atlantis, and I need you working in that capacity instead of my glorified secretary.”

“I am your XO,” Lorne said, still watching John warily. “That is part of the job.”

John snorted. “Not the way it’s been happening,” he said, shaking his head. “I’m going to be taking over my duties again so that you can focus on yours.”

“You sure?” Lorne asked, and John watched as his XO chewed his bottom lip, looking at John with a narrowed gaze.

John knew that Lorne reported to O’Neill, he had guessed that quickly enough, and he didn’t mind. He had expected to have someone watching over his shoulder. He wondered if it was his black mark or his bowing to Elizabeth that had made O’Neill put a spy in his command. He realized it was probably a combination of both. He was irritated, but he also wondered if there was some way he could use it to his advantage. Lorne kept watching him, and John looked back evenly, wondering what the man was thinking and wondering if he should ask.

Lorne finally spoke. “It’s complicated out there. There are so many moving parts, and we don’t have the same safety net we do in the mountain. This whole city is a science experiment, and so there’s always an element of danger. It makes science just as important as the military, and it’s all based on the situation. There’s a lot of gray areas.”

John nodded. “I know, and I’m going to pay attention and do my job, even if I don’t understand Elizabeth right now.”

Lorne hummed noncommittally. “You know I listened to the recording of the Doranda mission?”

John glanced up and raised his eyebrows, waiting for Lorne to continue.

“She’s the pilot who won’t bail out even when things have gone wrong. She’s holding onto something, hoping she can right it,” Lorne explained. “The Doranda mission changed things, and she can’t accept it, even though she needs to.”

“But she’s not,” John said softly. “She’s fully prepared to crash into the ground right now and can’t see the writing on the wall.”

Lorne nodded, looking at John with what he thought was a little bit more respect. “I just hope she doesn’t bring us with her.”

“This is a bad plan,” Ronon said, watching as Ellis beamed back to his ship.

John nodded and leaned against the railing, face blank as he looked down to where Elizabeth and Carson were standing where Ellis had just been. It had been three days since Ellis had shown up with orders from General Landry and the IOA to capture a Wraith for Dr. Beckett to study and proceed with his experiment.

General O’Neill had ordered him to help prepare the marines, but that he wasn’t to go. John had felt such an immense amount of relief that if he hadn’t been sitting already, his knees would have buckled. They had captured a Wraith once when they were new to the galaxy, and the Wraith didn’t know who they were, and they didn’t know how dangerous the Wraith were.

John had spent the last three days working with Ronon and Teyla to prep the Marine team charged with capturing one. He had been a little bit surprised when they had gone along with what he had said without argument, at least until one of them told him General Everett had handpicked them. Seeing the General was a quick lesson to everyone.

“I feel like we should go with them,” he said softly. “But I don’t want to put anyone in danger.”

The marines might have listened to him and Everett, but that didn’t mean they were prepared to go out and face the Wraith. The Wraith might prefer to stun their victims, but they had no problems killing when needed.

“You can’t,” Ronon said. “You have orders.”

“Not like I haven’t disobeyed them before,” John said, rocking on his heels and trying to calm down. “It’s how I ended up here.”

“That’s not an order you can disobey now,” Ronon said. “Not after you told Weir you didn’t need her help anymore.”

Ronon and Teyla had both been pissed off and were both still pissed off about the whole situation. Teyla had tried talking to Elizabeth, but Elizabeth had shut her down. Ronon had just shut out both Carson and Elizabeth completely. John didn’t blame either of them.

“I know,” he said, rubbing hands over his face and leaning against the railing. He felt Ronon bump his shoulder, and he looked up at his friend, who was grinning.

“I’m not your military,” Ronon said. “Not technically. Most of them think I’m stupid, can say I didn’t understand if I went.”

“I’m not going to ask you to go,” he said.

Ronon nodded. “I know.”

There was a long moment of silence, and John kept his eyes on Ronon, wondering what was going on in his mind, and John was so grateful for Ford for choosing that planet and allowing them to run into Ronon. He missed Ford, and the kid was another in the long line of failure John felt. But finding Ronon was like finding the missing piece of the puzzle. He fit in a way Ford never had, and John hated himself for that thought.

Eventually, Ronon stood up and stretched, twisting his back. “Tell Ellis I’ll be ready in ten.”

John nodded, watching as Ronon jogged off, no doubt to get his own sword. He tapped on his radio, asking Chuck to transfer him to the Apollo.

“Colonel Ellis?” he asked, waiting for a reply.

“Yes, Colonel Sheppard?”

“Ronon has offered to come if your marines would like some aid,” John said, dropping his head into his hands to rub over his face.

“Any help would be appreciated, thank you, Colonel,” Ellis said, and John could hear the relief in his voice.

He blew out a breath. “He’ll be ready in 10. Chuck will let you know when he’s ready for beaming.”

Ellis signed off, and John raised his head, looking down to see Elizabeth watching him for a moment before she made her way up the stairs to come and stand next to him.

“Still not going, Colonel?” she asked, a hint of something snide in her tone.

Ever since he had backed Rodney, their relationship had been more strained, the two of them acting like a divorced couple during Christmas for the kids. A feeling John knew all too well from sitting through his Dad’s multiple divorces over the years.

“Ronon is going. I have orders not to assist,” John said evenly, looking at her, keeping his temper in check.

“Because you told General O’Neill a lie,” Elizabeth snapped, not bothering to keep her voice down.

“Dr. Weir,” John said, standing up. “If you wish to have a discussion, perhaps we can take it into your office for privacy?”

She looked around, noticing the people watching them, and flushed slightly, turning and walking into the office without another word. John glanced around the room, most people avoiding his eye contact. He sighed and followed, waiting for the door to close, crossing his arms.

“I didn’t tell the General a lie,” John said before she had a chance to talk. “And I’d ask you not to make such baseless accusations in the future.”

“What did you tell him then?” she demanded.

“I told him that I was not comfortable sending my men to capture a Wraith on an experiment that I thought was happening too soon,” John replied, falling into parade rest out of habit.

“That you disagree with,” she snapped.

“No, that I think is premature,” John corrected. “I think that it’s been less than six months since I was affected by the retrovirus, and if people smarter than me have issues with it, then that’s something to consider. I don’t want another Hoff situation, do you?”

“It’s not the same!”

“Why?”

“Because it’s the Wraith!” she snapped, throwing her arms up in the air. “You and Rodney are acting like the Wraith are people and that we should treat them the same as we would people. But they’re not. They’re different.”

“So is Teal’c from my understanding, so are the Asgard, doesn’t mean we should ignore the fact that they’re sapient. Rodney was right on that, and you know that,” John said. “The only difference is that the Wraith are our enemy.”

“They want to eat us.”

“Yes, and they need to eat and we’re their food source. It sucks and it’s terrifying but that isn’t a crime.”

Elizabeth sat down at her desk with a thud, and John could see her hands were shaking a little bit. He waited a second before he moved to sit down across from her, crossing an ankle over the knee and leaning back, trying to appear relaxed. “The problem I’ve found with Pegasus,” John started slowly, waving a hand in the air, “is that it is hard to look at your Earth-based morals and hold onto them when the rest of the ground is shaking under you.”

Elizabeth glanced up at him but stayed silent, and John sighed. “As far as I’m concerned, morally, if they’re sapient, then we shouldn’t experiment on them. However, I also understand the need to figure something out because the Wraith are truly our enemy in a way we’ve never had to contend with before.”

“We need to do this.”

“No, we don’t, you just want to do this because if it works, and if they’re human, and if they continue to fight, you can shift the blame for xenocide from your shoulders,” John said gently. “But that’s not how that works. We go down this path; it’s still our fault.”

Elizabeth turned her head to the side, looking out the window, her jaw set and hands clasped together. John wanted to shake her, to do something to get through whatever fear blockade was stopping her from thinking. He didn’t know what he could say, and he didn’t want to argue over the same thing time and time again.

“Elizabeth—”

“—Colonel Sheppard, I have work to do if you don’t mind,” she said, turning towards her keyboard, a clear dismissal.

John sighed and stood up. “I’m here if you need to talk.”

Elizabeth didn’t say anything, and John didn’t expect her to, and so he left as she started typing.

John dropped down into the chair in his office and rubbed a hand over his face before tapping his radio to let Lorne know that Ronon was going with Ellis. Teyla was with her people, she was furious with Elizabeth over not being told, and John couldn’t blame her. His team was on stand down until the Wraith experiment was done. No one wanted the CSO and CO off-world right now.

“Lieutenant Foley,” John called, waiting for one of the rotating aides Lorne had started employing from the younger officers to stick his head in the office. “Give me whatever paperwork Lorne’s given you, and then take the day.”

The Corporal looked at John for a second, confused, before deciding that it was better not to ask, and nodded. A few minutes later, John had the tablet in front of him. He could feel the regret already, but he knew if he didn’t have something to do, he would wander around, making a nuisance of himself. He had been told by Lorne a couple of times that ‘the men get nervous when you watch them, sir, so try not to make it a habit.’

He managed to get halfway through it before the door to his office slid open, and he glanced up after signing the requisition to catch sight of Rodney standing in the doorway, looking pissed off.

“What’s up?” John asked, looking down to file the paperwork before saving everything. He dropped the pen on the desk and crossed his arms over his chest.

“I don’t like this,” Rodney said, stepping inside and letting the door close behind him. “At all.”

“I know, but it’s above my head now,” John said, rubbing the side of his neck. “Colonel Ellis is going to be dealing with all of it. Capturing, security, the whole thing. We’ve cleared the wing Carson is going to be working in and added extra security so the Wraith can’t get to us.”

Rodney dropped into the chair across from him, still looking tense. John tried his best to relax, to look like this was normal, that there was no gulf between them. He knew their problems hadn’t magically disappeared with the apology, and he wanted to tread carefully, not wanting to slide back.

“I know that,” Rodney said after a couple of minutes of silence. “I just think it’s premature.”

“I know, I agree,” John said, thinking back to the arguments in the conference room. “But what else could we do?”

“I think we have some cyanide around,” Rodney offered with a small smile. “Slip it in, none the wiser?”

John grinned but shook his head. “Too obvious, and it’d show up on the tox report during the autopsy.”

Rodney sighed and sunk down into the chair, looking out the window that had been the main reason John had wanted this office. They were high enough that John had a good view of the ocean stretching out for miles, the view unimpeded by the towers. John had spent a lot of his life by oceans, and he never got over the view of the sea, the way the sun made it sparkle. If he leaned back in his chair, then he could almost imagine flying.

“I want this to work,” Rodney said quietly. “Don’t get me wrong, I do. I just don’t want another Hoffan situation.”

John nodded. “I know that.”

“Does anyone else?”

John wanted to deny it, but he knew he couldn’t. He knew Elizabeth was confused by what Rodney wanted and scared enough to want to go along with whatever Carson was proposing. Carson was so caught up in the thrill of discovery that he was having trouble stopping and taking his time to think.

“They’re scared,” John said. “They want this to work because they’re scared. The Siege changed a lot of people’s minds, and sure they might have stayed, but they’re more aware of the stakes than before. They’re terrified of the Wraith, but they’re excited about the discoveries, and so they’re grasping at straws so they can keep on exploring.”

“Exploration is always dangerous,” Rodney said quietly, looking out the window for another few seconds before looking back at John. “It’s not the right solution. It’s a solution, but it’s not going to fix a lot of problems. The Genii aren’t the Wraith, and the Dagans chose to side with them instead of with us. The humans here are just as much of a problem.”

“I know.”

John slouched down in his seat, fingers fiddling with a pen he grabbed. “Humans.” He stopped for a second and sighed. “We know how to fight humans, as shitty as it is. War is normal for us. We know how to kill other humans, and we know how to fight humans. It’s the alienness of the Wraith that causes the issues.”

Rodney sighed. “’War must be, while we defend our lives against a destroyer who would devour all.’”

John tilted his head to the side. “What’s that?”

“Tolkien,” Rodney said with a smile, looking up and pinning John with an intense look. John wanted to fidget underneath it, wondering what Rodney saw, and instead, he made himself stay still, looking unconcerned.

“Thank you,” Rodney said finally, looking back out over the window.

“For agreeing with you?” John asked, confused.

Rodney shook his head and stood up, a hand rubbing at his back as he twisted. “No, for apologizing for when you were in the wrong. You’re the only one that’s done that.”

There was something there that John wanted to ask about, but he knew that it wasn’t the right time. He tilted his head a little confused but nodded. “You’re welcome.”

Rodney nodded back and left as quickly as he had come, leaving John to slump back down in his chair. Before, the two of them would linger, talking instead of going back to work. But Rodney coming to his office to talk to him instead of yelling was a start. He looked over at his locked drawer, where the copy of the birth certificate was, and sighed, leaning forward to start the paperwork back up again.

One step at a time was better than nothing.

Four

“I don’t think that’s such a good idea. We still don’t know if there are any residual effects from the retrovirus,” John said, his back tense as he looked around the room.

Carson wouldn’t meet his eyes, and Elizabeth was looking at him triumphantly. Teyla looked uncomfortable, her eyes on the table. John wanted to know what the hell she was thinking trying to befriend him. Out of everyone, he wanted to know what was going on in her mind the most.

Elizabeth kept his gaze, but she spoke to Kate, and John clenched his jaw, not backing down. “What do you think, Doctor? Is he ready to join the community?”

Kate looked thoughtful for a moment, and he wanted to shake her. John wished that Rodney was here to yell at all of them about how stupid they were. But the IOA had made it very clear that if Rodney didn’t want to be part of the experiment, he had no say, so he had been kept out of the meeting. John was still pissed off.

“A change of scenery could be very beneficial to him,” Kate said, nodding her head.

Elizabeth looked triumphant, and she nodded. “Good, release him.”

“This is not a good idea,” he repeated, his jaw tense, shoulders back.

“He doesn’t remember anything,” Elizabeth snapped back.

“For now, can you promise me he won’t regain his memories?” John asked, looking at Kate and Carson, who both shook their heads. “You want to release him based on the assumption that he hasn’t regained his memories in the four days since his transformation finished. Four days.”

He wanted to slam his fist down on the table but fought back the urge.

Ellis spoke up. “Colonel Sheppard, your disagreement has been noted, but this is a—”

“—military issue. The safety of this base is my responsibility, and not a single person here can overrule me on this,” he said, looking around the table, waiting for someone to say something. Even Ellis stayed silent.

“Reintroducing him into the general population will serve him well. If we keep him isolated, it could cause anger and mistrust,” Kate said, looking at John with the same sympathetic look she always had. John hated it.

“Then you wouldn’t mind showing him around,” John returned easily, glad when her face paled. “After all, I think having a psychiatrist would be good for him, to help him be reintroduced?”

He raised an eyebrow, daring her to argue. She averted her gaze and sat back, not saying anything else. John felt that he had made his point.

“Colonel Sheppard,” Elizabeth said, her voice the smooth tone John associated with her making treaties. “I understand your hesitance, but surely you can see the benefit of allowing Lt. Kenmore to—”

“No,” he interrupted. “No, I cannot. I don’t see a single situation where allowing an enemy combatant to wander around the city four days after we’ve finished experimenting on him is a good thing. Perhaps, if you do want him to be reintegrated, he should start on the Apollo. Colonel Ellis, you seem to think he’s fine. Do you mind if he goes onto your ship?”

John looked over at Ellis, who suddenly looked uncomfortable. “He doesn’t have the clearance.”

“And he does for Atlantis?” John asked, leaning in slightly, gaze hard and angry as he watched Ellis.

Eventually, Ellis looked away and shrugged. “Perhaps we could wait a few more days.”

“Sheppard!” Elizabeth snapped. “He is being released, and you can either get with the program or leave.”

John stood up, pressed his hands on the table, and leaned over, not caring at the sudden fear he saw in Elizabeth’s eyes. “Dr. Weir,” he said softly. “You are not my CO, you are not in my chain of command, and you are not in a position to overrule me regarding the safety of Atlantis. The Wraith will remain in isolation for a full two weeks at minimum to make sure that nothing else is happening.”

He turned his head, looking at Carson. “Unless you want to run the risk of killing fifty percent of Atlantis?”

John knew it was a low blow, and Carson flinched away, looking to the side. He looked around the table, one by one, everyone angry but no one questioning. John tilted his head in surprise at the look of relief on Teyla’s face and made a note to talk to her later. He sat back down and looked over at Kate, who was still pale.

“Dr. Heightmeyer,” he said, waiting until he had her attention. “It is now your job to work with him and make sure he understands that this is not punishment, that we want him to be safe.”

“Do you want this to work, Colonel?” Elizabeth demanded, face pale with anger. “Or do you want to see us fail?”

“I want this to work just as much as everyone else, more so in some cases. It was my actions that woke them up, and I have to live with that,” John returned evenly, keeping his temper in check. “I don’t want to put the lives of the entire base at risk because of it. And it worries me you’re more interested in the Wraith than you are in the well-being of the people you keep telling me you’re in command of.”

Elizabeth’s face went white, but she didn’t reply, and John turned to Ellis. “I expect to have teams of your men sent down to help guard the Wraith.”

“Security is your job,” Ellis replied smoothly.

“No,” John said, smiling with what his Dad used to call his ‘fuck you’ smile, “As per the IOA instructions, the security and handling of the Wraith is your job. However, I know your men aren’t familiar with Atlantis, and so I think one of your teams and one of mine working together would be a good middle ground.”

Ellis nodded his head after a few seconds. John looked around the room, seeing multiple glares directed at him, but no one else commented. The meeting broke up a few seconds later. Ellis stayed sitting, and John waited until the room cleared before raising an eyebrow at Ellis.

“You’re making enemies,” Ellis said, the anger mostly hidden now.

“Why?”

“If you keep fighting what the IOA wants,” Ellis started and stopped when John shrugged and sat back down.

“Let’s run through this. Say I’m wrong, and this is the magical fix for the Wraith. Do you think anyone will get mad at me because I was concerned about the base’s safety? That sets a bad precedence, and you and I both know it,” John said, waiting until Ellis nodded his head reluctantly.

“And if you’re right?” Ellis asked. “What happens then?”

“Then hopefully no one dies. And you’ll leave,” John said, shaking his head when Ellis started to speak. “You and I both know you won’t stay to fight this war. If it turns bad, then you’ll be called back, leaving me here to deal with the fallout.”

Ellis slumped back and sighed. “I have my orders.”

“I know,” John said, rubbing the side of his neck. “I know you won’t go against them. But the safety of this base is my first responsibility, and I’m not going to forget that. Not unless I’m dead or relieved of my command.”

Not again, he told himself. Never again.

“Dr. Weir has powerful friends,” Ellis said, all of the anger gone, replaced by the look of someone stuck between orders and the right thing. John knew that position well, and it was the reason he had a black mark.

John bit the inside of his cheek as he regarded Ellis. “Permission to speak freely?” he asked after a moment.

Ellis tilted his head to the side. “Considering how freely you’ve been speaking I’m interested to hear this,” he said, looking amused which John was thankful for. “Go on.”

John shrugged. “She might have powerful friends, but I frankly don’t give a flying fuck. The problem with this base is that the scientists outnumber the military. And every single one of them gets caught up in the idea of discovery. And it’s great. There have been discoveries that will change the world for the better. But it’s my job to contain the bad ones. And like I said, until I’m dead or relieved of command, then I’m going to do my best to make sure no one else dies.”

Ellis was silent for a long moment before he nodded his head. “I don’t disagree with you about any of that. But, you need to watch your back. Atlantis needs someone like you here. I’ve seen what happens when science gets the best of people at the SGC, and you’re far from home.”

John felt a little of the tension leave his shoulders at Ellis’s admission, and he nodded his head. “We were alone for a year, Colonel. I know that very well.”

John gripped the tablet and did his best not to throw it across the room. He could see Lorne tense up, and he wondered what was on his face that made his XO look one second from grabbing a grenade launcher.

“Problem, sir?”

John ground his teeth together and nodded, looking back down at the email he had gotten from O’Neill and started reading. “Sheppard, orders from above me. Drs. Beckett, Weir, and Heightmeyer have control of the Wraith Experiment. You are to aid and assist as needed and do your best to make sure it succeeds. This is bullshit, but it’s from someone above my pay grade. Support as they need, but don’t for one second let your eye off the safety of the city. I’ve got your back.”

John dropped the tablet down onto the desk and pressed his forehead against the wood, taking a couple of deep breaths to try and get himself under control. He felt angry, the sort of rage he hadn’t felt since the Genii had stormed his city, but even that seemed to pale in comparison to what he was feeling right then. He raised his head and looked over at Lorne, glad when his XO seemed to be as pissed off as he was, his mouth pulled down.

“Get McKay,” John said, feeling like he forced each word out. Lorne nodded and contacted McKay for him as John tried to get himself under control, feeling like his skin was too small for him right now. It didn’t take McKay long to get here, stalking in with snapped ‘what’ that cut off when he noticed the tension in the room.

John didn’t raise his head, just grabbed the tablet and held it out for Rodney to read. He kept his eyes on the desk, taking deep breaths in and out to calm himself down. It wasn’t working.

“What the fuck?” Rodney said, his voice soft with shock. A thump sounded, and John forced himself to look up, watching Rodney slump in the chair.

“Yep,” John said, sitting back up, leaning back in his chair, and doing his best to calm down. “She contacted the IOA two days ago to make a complaint after the meeting. We just got this data burst this morning.”

“Oh good, so now we’re wasting power,” Rodney muttered, pinching the bridge of his nose. “So what now?”

John shrugged. “It’s an official order. I have to go along with it.”

“But it’s bullshit!” Rodney snapped. “They’re putting us all in danger!”

John sighed, looking over at Lorne, hoping for something, but his XO just shook his head. “Right,” John said, leaning forward and clasping his hands together. “Did you know Ronon was a Military Scientist on Sateda?”

The non sequitur got their attention, and Lorne and Rodney looked at him, waiting for him to continue. “Right now, Ronon is a military contractor, which means he’s supposed to follow my orders. There’s some leeway there because he’s not an Earth native, but not enough. I want you to draw up a new contract for him to be under you,” John explained, looking at Rodney. “I have to order my men to go along with this, but if Ronon is under your umbrella, he doesn’t have to follow my orders.”

“For what reason?” Rodney demanded.

“So we can have him watching out for the Wraith outside of the official orders,” John said with a shrug. “Not perfect, but it’s the only way I can do anything right now.”

Rodney nodded his head, looking as pissed off as John still felt. “Send him to me in 20. I’ll have the paperwork. We’ve got something for Alien contractors that’ll work.”

John nodded, feeling paranoia raise its ugly head. “Can you encrypt my tablet?” he asked, not liking that the IOA was going over his head with this. “Just in case.”

Rodney paused in the middle of standing before he nodded his head. “Yeah. Give it to me later and I’ll do it,” he said as he finished standing.

John nodded as Rodney left, looking over at Lorne, who watched him with a little more obvious respect than John was used to seeing. “Get everyone into the marine common room. I want every single person to know exactly what I expect out of them.”

John folded his arms across his chest, watching the feed on the screen as Teyla showed the Wraith around his room. He wondered if he should start calling the Wraith Michael. He grimaced, glancing around the room they were using to monitor Michael. Carson and Elizabeth looked excited, and Kate looked wary but hopeful. Ronon wasn’t here. He was helping Rodney with something to keep up the illusion of being part of the science department. The move had raised a few eyebrows, but no one had commented.

John frankly thought Elizabeth’s smug look anytime she looked at him was a bit much, but he bit the inside of his lip and kept quiet. Only Ellis looked at him with sympathy, understanding how John was chafing under the orders.

Teyla said goodbye and left. John followed, not wanting to deal with Elizabeth’s smug look anymore. He made sure the marines stationed outside the door knew what their orders were before finding Teyla. He caught up to her a few hallways over, leaning against the wall, her face in her hands.

“You okay?” he asked, leaning against the wall next to her. “You don’t need to do this, you know.”

Teyla was silent for a long moment before she nodded. “Thank you, John, I know. But I want to do this.”

She dropped her hands away and smiled at him, and he nodded. “Why are you doing it?” he asked softly, needing to understand why.

“Because it’s a chance, John,” Teyla said softly. “A chance to end this war and I have to help however I can.”

He felt a hand on his arm, and she smiled. “I know you have your issues with it, and I understand, and I agree. Your priority should be the safety of this base, and you are doing it justice.”

“I am now,” he muttered. “I suppose now is as good a time as any.”

Teyla shrugged. “Perhaps. But I am doing this for my people, for their chance. You do understand, right?”

John nodded and looked down the hallway. “I understand. I want this to work, just as much as everyone else,” he said. “I just don’t want to rush it.”

Teyla just nodded her head and pushed away from the wall. “I know why we are lying to him, but it still feels dishonest, and I am worried what will happen when he does find out.”

“You think he will?” John asked as they started walking.

“I think in a city this size, with this many people, it is inevitable.”

“I don’t want to talk to the fucking Wraith,” Rodney muttered, moving another pawn.

John looked up from the board. Neither of them was playing their best right now. John was moving pieces without thinking, and Rodney had made an illegal move with his bishop that John hadn’t bothered calling him on. He stayed silent, letting Rodney talk out whatever he wanted to say.

“I don’t want to, but I have to,” Rodney said with a sigh. “Everyone thinks I don’t want this to work, but I do.”

“Same here,” John said softly. “It’s not black and white.”

“Tell that to everyone else,” Rodney said, reaching out to lift a white and black pawn from the discard pile, holding them in his hand. “Elizabeth is still pissed at me, so I don’t think that helps.”

“You still mad at her?” John asked, taking one of Rodney’s knights, ignoring the obvious checkmate so they could spend more time together. John was still taking the little moments he could get, soaking them up like the last rays of sunshine in winter.

“Yes,” Rodney said. “But now I’m mad at how stubborn she is. She’s digging her heels into the sand, fighting something that doesn’t exist. We’re not fighting with her over everything because we hate her and want to bring her down. We’re fighting this because we want what’s best for the city. She’s paranoid. ”

John nodded his head and leaned back, stretching his legs out in front of him, crossed at the ankles, feeling Rodney’s legs brush against his own. “I know.”

Rodney glanced up at him and then looked back down, nodding his head. “I suppose you do.”

John smiled and nodded towards the board. “Your move,” he said, crossing his arms over his chest and watching Rodney as he looked at the board intently.

It took a few seconds before his look changed to one of disgust, and he reached out, knocking over his king. “Stop giving me the games. If I’m playing like shit, call me on it.”

“Felt bad. It was like taking candy from a baby,” John said, nodding towards the chessboard. “Again?”

It was getting late, but John had come to love these quiet moments between the two of them. Everything on the city was so fast, and it only seemed to be getting faster. Carson was excited and working hard, trying to track as much of Michael’s progress as he could. Teyla and Kate were helping with integration, and Elizabeth was walking around looking smug.

Ellis had been the surprise, coming and talking to John about the base security, as well aware as John was about the danger.

“How bad is this going to become?” Rodney asked, reaching out to begin to put away the pieces.

John felt a stab of disappointment but started to help anyway, keeping his eyes on the board so he wouldn’t have to meet Rodney’s gaze. “Want my nightmares or my dreams?”

“I think a man’s dreams should remain private,” Rodney said primly, and John half-smiled. “So nightmares.”

“He remembers and goes on a killing rampage,” John said simply. “I have more guards on him than the president right now, but there’s always the possibility.”

Rodney nodded and folded the board up, putting it into the carrying case before he sat back. “Sounds like mine.”

“I want this to work,” John said, repeating what Rodney had said earlier. “I do. I don’t think it’s going to be sunshine and roses. He’s one person, and we don’t know how different each Wraith hive is from the other. There could be no differences, or it could be as different as the Asgard are from us.”

“Elizabeth accused me the other day of being an overthinker who destroyed dreams,” Rodney said with a grin.

“Has she met you?” John asked with a smile.

Rodney snorted and stood up, putting the case away and nodding towards his laptop. “Want to watch something?”

John knew it to be another olive branch, and he nodded his head quickly. “As long as it isn’t science fiction.”

Rodney grimaced. “I used to love all of that shit,” he said, clearing the table and grabbing his laptop. “But the last few months have changed my mind on it.”

It might be an olive branch, but it was a small one since they would watch on the table instead of on the bed as they used to. John would take it and moved his chair around to settle next to Rodney, stretching his legs out in front of him and relaxed, slumping to the side, so their shoulders brushed.

“Same,” he said. “Now I watch it, and all I can see is requisition forms dancing in my eyes. So much clothing wasted on knives and nails.”

Rodney laughed and sat down, pressing play on the screen. “That’s rich coming from you. I’m surprised you have clothing half the time.”

“Mix and match,” John said, looking down at his shirt. “One of the perks of standard military issue, I can use the sleeves from one shirt on another, fix some holes, hem something.”

Rodney glanced at him and grinned, wide and bright. “You know how to sew?”

John nodded. “I’ve spent a lot of my career in the middle of nowhere. I learned really quickly how to keep clothing on my back.”

“Well, I know who I’m going to go to when I need something darned,” Rodney said.

John knocked his shoulder against Rodney’s but didn’t deny it. He was pretty proud of how handy he was with a needle and thread.

Rodney leaned back in the chair after hitting play, and John felt the pressure on his shoulder increased. He kept his eyes on the screen, wanting to keep it casual at the moment, but he didn’t stop the small smile from drifting across his face.

John settled in, half leaning against Rodney. “What are we watching?”

Rodney stilled for a moment, and John could see him turning his head out of the corner of his eye. He forced himself to stay relaxed, waiting for Rodney to make the next move. When he didn’t move away John hid a smile.

“Dogma,” Rodney said, reaching out to hit play.

“Good, I could use a laugh.”

Elizabeth glanced around the room before looking back at Teyla. “He’s only had the one dream?”

Teyla nodded and folded her arms across his chest tightly. “Yes. He believes the Wraith did something to him during his capture.”

“So he’s remembering,” Rodney said.

John looked over at Carson, who was watching the monitor worriedly. “Carson?”

Carson shrugged. “Maybe,” he said. “We knew this might be a possibility. It could just be a dream.”

“Or it could be him remembering,” John repeated, copying Rodney. “What can we do about it?”

“I could increase his dosage, although I recommend against it at this time,” Carson offered.

“Why?” Rodney asked. “He’s clearly remembering, so why wait until something else happens?”

“It’s calibrated to him, and if we change it too much, it might stop working. If it’s merely psychological, then Doctor Heightmeyer should be able to help him through it.”

“I don’t want anyone with him alone. I’m doubling the guard,” John said, looking over at the monitors, where Michael was sleeping. “No discussion.”

“So now what?” John said, leaning against the conference table, too amped up to sit down. He looked around the room and raised his eyebrows when no one spoke. “Let’s not all speak at once.”

“It worked,” Elizabeth said, leaning forward. “We can change all of them.”

“For a week and a half,” John snapped back. “And then what? Do we keep redosing them? How is that a good idea?”

“So it needs some more work.”

“No shit, but what do we do with the Wraith we have right now,” John said, looking over at Carson. “Doc?”

Carson sighed and rubbed hands over his face. “Kate says he’s still experiencing Wraith compulsions, the need to feed and the like. I dunnae if they’re psychological or if his feeding mechanism is returning.”

“And if we up his dose?” John asked. “Will that work?”

Carson shrugged. “If we keep upping his dose, we run the risk of him developing an immunity to the virus, and it stops working altogether. He might be remembering, but his physiological changes are still stable. And there’s no guarantee that the next time he won’t remember. The brain is a funny thing.”

“So what?” Elizabeth demanded, her voice a little higher. “That’s it. We’re done?”

“It’s dangerous to keep him here,” Rodney said, speaking up for the first time from where he was watching the monitor. “The Wraith are a telepathic species. If he’s remembering, we can’t guarantee that he won’t be trying to reach out to the hives, and that could bring them to us.”

Ronon cleared his throat. “Your experiment didn’t work. We should kill him right now before he brings anyone to us.”

“We can’t kill him, Ronon. We’re the ones who put him in this position,” Heightmeyer said, and John grimaced, turning his head to the side.

“You only have an issue with it because he looks human, but he’s not. He’s the body of a human with the mind of the Wraith. We wouldn’t think twice about it if he still looked Wraith,” Rodney snapped.

“But we did give him the retrovirus. We made him human. Now we have the responsibility to treat him as we would any other human.”

Ronon snorted and shook his head, looking as pissed off as John felt. “He’s not human. He’s a Wraith.”

“We’ve come too far to abandon it,” Elizabeth said, speaking up, her hands clasped in front of her and looking as stubbornly determined as she had been for the past few months. John dropped his head down with a sigh. “Carson, I want you to increase his dosage and see what happens.”

“Dr. Weir,” John said, looking over at her and trying to keep his voice calm. “The retrovirus doesn’t work. It failed.”

“No, it didn’t! It needs more work, and the only way to fix it is to continue with the experiment,” Elizabeth snapped as Heightmeyer nodded.

“We must try and help him as much as we can. It’s only fair after what we did to him.”

Rodney snorted. “Good to know that you’re against killing, but you’re okay with illegal human experimentation Dr. Heightmeyer.”

Kate flushed and looked to the side. “It’s not the same.”

“Oh yes, it is. If you’re against killing the Wraith because he looks human, then you should be against experimenting on him, but you’re not. You know he’s a Wraith, you just don’t want to have blood on your hands, but if we keep experimenting on him at some point, it’s going to fail. It’s a fucking miracle he survived this at all,” Rodney snapped. “Stop falling back on bullshit excuses and own up to your decisions. There is no guarantee he will be able to handle more of the experimental retrovirus we’re shooting him up with.”

Kate flushed even more and looked back at Rodney, looking like she was about to argue before she slumped back and nodded her head. “You are correct, Dr. McKay,” she said, sounding worn out. “But, I cannot condone killing him. I understand that it’s a question of semantics, but I am not comfortable killing in cold blood.

Ronon let out a bark of harsh laughter. “Tell that to the children of Sateda who were drained of their life.”

“Enough,” Elizabeth snapped, looking around the room before settling on Carson. “You will up the retrovirus to see what happens.”

She looked around the room, her chin up and daring anyone to say anything. “This experiment is going forward with the full backing of the IOA, and no one has the authority to do anything about it.”

John wondered how long it would be until she noticed that the more she said full backing of the IOA, the less weight it carried.

“Drop your weapon,” the Wraith said, pointing it at Cole, who was glancing between John and the Wraith, shoulders tense and fingers tight around the trigger guard.

“You drop yours,” John said, grimacing as he pointed the stunner at the man, seeing the same blood lust and frenzy he saw in the Wraith.

“Just take it easy, Lieutenant,” Cole said, trying to be reasonable.

The Wraith hissed, the noise sounded odd coming out of a voice box that was more human than it had been. “Stop calling me that. Drop your weapon!”

John could feel how tense Ronon was next to him, and he could hear his rapid breathing. He was just glad Ronon hadn’t drawn his gun yet, letting John deal with it. John should shoot. No one would blame him. The Wraith was holding Cole at gunpoint.

“What do you want me to call you?” John asked, trying to keep his voice calm and even to diffuse the situation.

The Wraith looked at him and hissed again. “I don’t remember! You took my memories! They were mine, and you took them from me!”

“We were trying to help,” John replied, but even he knew that it fell flat. He remembered the conversation Teyla had with the Wraith when he started remembering. The Wraith wasn’t wrong, they had done it for themselves. “We just wanted to help.”

“Help yourselves,” the Wraith replied, looking at the stunner in John’s hands. Before John could act, he raised the gun and shot Cole, jerking back a second later as red light hit him twice before hitting the floor. Teyla shoved past him, running to Cole, and John turned to Ronon.

“Ronon holster…,” he trailed off when he saw that Ronon didn’t have his gun out.

Rodney stood there, slowly lowering Ronon’s gun, looking terrified and angry. John shouldered past Ronon and grabbed the gun from his hands, turning and looking at it set to kill. His hands dropped to his side, and he looked up at Rodney, who watched him evenly, unrepentant.

“Experiment failed.”

“He’s dead,” Teyla said, her voice shaky and John turned to look at her, a hand pressed against Cole’s chest, the marine’s eyes wide and sightless, blood pooling around him.

“You shot him!” Elizabeth thundered, slamming both hands on the table and glaring at Rodney, who sat, both hands folded across his stomach and seemingly unbothered at Elizabeth’s temper.

“Yes.”

“You had no right,” Elizabeth hissed, her face as pale as John had ever seen it.

Rodney rolled his eyes and shook his head. “He was a danger, and I did what needed to be done,” he said, and John wondered if Rodney felt bad by it or not. He didn’t act like he felt bad. Rodney acted like it was another day of fighting the Wraith. John hoped that he was fine because John knew he wouldn’t lose a single moment of sleep over the whole situation.

“He was our chance to end this war,” Elizabeth said, one hand flinging out to the side. “We had agreed that Carson would up his retrovirus and see what happened.”

“And that changed when he stole a gun and pointed it at one of the marines!” Rodney snapped back, leaning forward finally.

“You could have stunned him,” Heightmeyer said, her voice quiet and small, shaken by the whole thing. “You didn’t have to kill him.”

Rodney’s eyes snapped to her, and he scowled. “He lost the right to be stunned the instant he shot and killed Sergeant Cole, or did you forget that an actual human being died trying to defend this city from a Wraith.”

The last was directed towards Elizabeth, who just scowled back. “What happened with Sergeant Cole was regrettable.”

Rodney shot up and slammed his hands on the table. “What happened with Sergeant Cole was avoidable! You kept pushing and pushing, Elizabeth. You had to have the Wraith out of confinement sooner. You, Carson, and Kate managed to convince the IOA to override Sheppard’s authority, and in doing so, someone died. Sergeant Cole’s death is on your hands.”

Rodney looked around at the three people, each of them looking shamefaced, and John shifted uncomfortably in his seat as Kate started to cry. Ellis was watching everything, face blank, but John was sure he could see some relief there.

“You are all so fucking worried about dealing with the Wraith that you’ll happily throw whatever you can into stopping it, no matter what the cost is. Or who,” Rodney continued, uncaring at the increasingly uncomfortable looks. Carson was pale and looking at the table, Kate was crying, and Elizabeth was looking like she was about to shake apart from anger.

“If you think for one second I regret killing the Wraith that was holding our city hostage, you are wrong,” Rodney continued, his voice a little bit calmer. “He shot and killed Sergeant Cole trying to get away. What do you think he would do if he had gotten away?”

Rodney’s eyes continued circling the room. “What information could he have gotten about us, about Earth’s location, if he had killed Cole and had left. Who could he have sent it to? We had a Wraith wandering the city under almost no guard, and it backfired, just like I said it would, like Sheppard said it would. Just like Ronon warned us.”

“Why did you use Ronon’s gun, McKay?” Ellis asked, speaking up for the first time.

“Because the IOA is going to lose their collective shit, and I’d rather deal with that than watch them try and sanction one of the few people in this room who has an even head on his shoulders. You and I both know that the majority of the IOA is xenophobic at the best of times. I shot him, so I’ll deal with the aftermath.”

“Don’t need protecting,” Ronon said, speaking up. “I can fight my own battles.”

Rodney sighed and nodded. “Yeah, but you don’t know how to fight Earth’s politics, I do.”

Ronon looked like he wanted to argue, but he settled for nodding, looking thankful.

“Doesn’t answer my question,” Ellis said.

Rodney managed a smile at that. “Smart,” he said, eyeing the man with a little bit more interest now, and John wondered what he saw. “Kills better, and quicker than a bullet. I didn’t know how much of his healing factor had come back, and I didn’t want to risk it, not while he was armed”

“You had no right,” Elizabeth hissed again. “The IOA will hear of this.”

Rodney snorted and leaned forward again, glaring at Elizabeth until she looked away. “Good.”

The simple confidence in his answer stunned John, and he looked over at Ellis, who had a satisfied look on his face. He raised an eyebrow at the man who shook his head minutely and looked away.

“Rodney was right,” John said, speaking up, finding his voice finally. “The only thing he was wrong about who needed to do it. It was a military situation, and I failed every person in this room by not taking that step. Rodney shouldn’t have been the one to kill Michael. I should have.”

John could feel that failure like a flashing light above his head. He was trying so hard to be better, be a better Commander for every single person under him, and he had failed a further time. He could feel the weight of that pulling him down, and he didn’t know what else to do. He couldn’t imagine being taken from the city, from being forced to leave Rodney, Teyla, Ronon, and everyone else behind.

Carson leaned forward and dropped his head against the table, shaking slightly, and Kate finally stood up, mumbling about being excused before she left, stumbling out of the room. Teyla nodded at John and followed Kate, and he was thankful for her help. He didn’t do well with people who cried.

“I will have your jobs for this,” Elizabeth said, voice low and dangerous. “The IOA will not stand by and allow this.”

“The more you say the IOA will not do something, the less power it holds,” John said, looking at Elizabeth as he stood up and gathered his things. “Try and take my job, Dr. Weir. I don’t care. I know the actions Rodney took were the right ones.”

With that, he turned and left, done dealing with Elizabeth and her stubborn refusal to learn.

“Colonel Sheppard.”

John had just gotten settled in his office and had sat down when he heard Ellis’s voice, and he looked up, trying not to show his irritation as he waved the man in, knowing he should stand up but not bothering. “I’m going to have a drink, join me?”

Ellis nodded and took the chair across from him, waiting for John to get two glasses and fill them with the whiskey he kept in his desk. And an old gift from his Dad for the bad days, a bottle he was whittling away at faster since he had gotten to Atlantis. It would be gone soon, and he’d need to talk to his Dad if he wanted to get more. That was not a conversation he wanted to have.

He handed it over and sat down, slouching in his seat with a sigh. “How much shit am I in?”

Ellis took a mouthful and shrugged his shoulders. “I don’t know,” he said honestly. “Honestly, you shouldn’t be at all. You made your objections well known in the beginning. You kept the Wraith under guard the whole time. You warned this might happen, and when it did happen, it was taken care of.”

“By McKay,” John said, fighting the urge to throw his whole drink back.

“Yes, but from my understanding, your orders were to keep the experiment going.”

John nodded his head and gave in to the urge to throw his drink back, feeling the burn before sighing. “And in the end, my Chief Scientist killed it.”

“Are you worried?” Ellis asked.

John thought about it before shaking his head. “No. I’m pissed off. I know I did my duty as best as possible, considering the stupid orders I was under. I’m just pissed off that Rodney was the one who shot him. I want to be better, the people here deserve it, but I keep feeling like I’m failing them.”

Ellis nodded his head and leaned back in his chair, swirling his drink around. “At the end of the day, that’s all any of us can do. Your men know that. It helps that people know McKay is difficult to work with.”

John’s eyes narrowed for a second, taking in the other man’s tone for a second before he shrugged, forcing himself to relax. “A lot of people also think I’m a wild card because I don’t believe in leaving men behind. Don’t take hearsay as fact. It never works out the way you think it does.”

Ellis tilted his head to the side and nodded, taking another sip of his drink. “Fair point.”

“So what can I do for you, Colonel?” John asked. “I don’t think it’s my whiskey and company.”

“The whiskey is good. Company’s not the worst.”

“One of the few things my Dad taught me that was useful. How to drink good whiskey,” John said. “Which, for the record, is not the way I just drank it.”

“What is the right way?” Ellis asked.

“When you’re making deals worth millions of dollars,” John said, reaching for the bottle and pouring himself another finger and leaned back and raised his eyebrows at Ellis, who finished his drink and set the glass down.

“I’m leaving in the morning, and I’ll be taking all the information regarding the experiment back with me. I have no doubt the IOA will have a thousand questions,” Ellis said, moving to stand up. “I would suggest you write your report and make sure everyone else has as well. Dr. Weir does have power, but she can’t fight a paper trail.”

John grinned a little bit. “No one can fight paper trails,” John said, setting the glass back down and standing up, reaching out to shake Ellis’s hand. “Thank you.”

Ellis nodded and shook his hand. “Good luck.”


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3 Comments:

  1. Most enjoyable. I was thinking that I needed some new McShep in my life, and voila, this really good story. So happy that Michael is dead.
    Love the little tendrils of friendship between John and Rodney. Just checking and hoping. Very nicely done.
    Thank you

  2. Yay! A dead Michael! Sweet.

  3. greywolfthewanderer

    nice one, well played!! dead Michael is the only good Michael.

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