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When The Levee Breaks

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“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?”


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?”


“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.


“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.