Title: Intervention
Author: Jilly James
Fandom: Stargate: Atlantis
Genre: Canon Divergence
Relationship: Gen, but can be read as pre-John/Rodney
Warnings: language, references to canon-typical violence
Rating: PG-13 for language and themes
Word Count: 3,367
Author Note: This is for the One Sentence prompt on Rough Trade. You can find the challenge here. The story takes place between The Siege Part, Part 3 (2×01) and The Intruder (2×02). I took some liberties with the prompt in that I have John on Earth when he has his unfortunate lapse in reason rather than thinking of returning to Earth.
Keira’s Response: Thirty-Eight
: John Sheppard is contemplating retiring and going back to Earth. McKay has quite a bit to say about that stupid idea.

Art by Polaris

– – – –

Rodney stalked out of the lab he’d co-opted while they were temporarily at the SGC, beyond fed up with the small minds trying to understand everything he’d done during their first year on Atlantis. It didn’t seem to matter to the scientist’s here—most of whom had never left the planet—that Rodney’s results were undeniable, they couldn’t stop questioning the why and how.

Part of him knew that was part of being a scientist, but there was an edge of…something about it that set him on edge. Now, he wanted pie, and he wanted Sheppard to sit across the table and listen to him bitch about it all. Which meant finding Sheppard, since he was the key part of this equation more so than the pie.

After ten minutes, he’d had no luck finding the errant major. The man had to be on base—none of them had been given leave yet as the debriefings went on and on. And on. The third person he asked finally pointed Rodney to the MWR room because, apparently, Sheppard needed to use a damn computer.

Rodney rolled his eyes and stalked off for the elevators. They’d come back from Atlantis with their laptops but most of them were still being reviewed by the SGC for some unknown reason. What did the SGC think they were going to find on their computers? Rodney’s had been released back to him already since he had the most urgent need for his own, familiar computer.

He spotted Sheppard using the farthest most terminal, though he didn’t appear to be doing anything, just staring at the screen. He was apparently so lost in thought that he didn’t notice Rodney coming up behind him.

“I’d have let you use a damn computer in my l—” Rodney broke off and goggled at what he was seeing on the screen.

Sheppard quickly cleared it, but the damage was already done.

“You’re res—”

“Rodney!” Sheppard hollered, stopping the indignant—and hurt—words that Rodney had been about to yell.

“What the hell, Sheppard?” He found his arm grabbed, and Sheppard led him out of the lab and down to the level of guest quarters where they had all been given rooms. There was no room on the permanent residence levels.

Sheppard shoved Rodney inside, and Rodney took a quick look around, finding it much like his own room.

He spun around and put his hands on his hips. “You’re resigning?!”

Sheppard glared then his expression shifted to something that Rodney couldn’t interpret. “I’m thinking about it, yes. Nothing is decided.”

“Why didn’t you talk to me? I thought we’d become…friends.” Rodney didn’t have many friends, so now he was wondering if he’d misread things. Not to mention other feelings that had come up lately. Things he wasn’t ready to look to closely at.

“We are friends, Rodney. This doesn’t have anything to do with you.”

“Then what does it have to do with?”

Sheppard sat on the edge of the bed, shoulders slumped. “I don’t think I can go back to Atlantis with Elizabeth in charge.”

“What?” Rodney was confused. “I thought you and Elizabeth got on fine.”

“We do. It’s not an interpersonal issue.”

“Then what is it?” Rodney grabbed one of the two chairs in the room and dragged it closer so he could sit across from Sheppard. “You know I’m shit at understanding all the nuance of stuff, so explain it to me.”

“The expedition charter makes it clear that Atlantis is supposed to be under military authority if there was found to be any exigent threat.”

Rodney frowned, vaguely remembering that, but he hadn’t given it any thought. “So why wasn’t it under your command all along?”

John shrugged. “I pushed at the charter at first, but Elizabeth made it clear she didn’t think I could actually…” he sighed. “That doesn’t really matter. Suffice it to say that I decided not to rock the boat while we were stuck out there with no way of contacting anyone. Besides, there weren’t really enough military assets. We were doing the best we could given the circumstances.”

“Yeah, of course we were. Really, we rocked the hell out of what should have been a lose-lose situation.” When John smiled faintly, Rodney added, “So you think when they’re planning for reinforcements that the expedition charter should be followed?”

“I do. We still need the science side of things, but, Rodney, too many scientists died out there. That should be raising more red flags her than it has. Yes, the SGC suffers some losses of civilian personnel assigned to gate teams, but it’s not that common. And they shouldn’t be so…callous about it. And that doesn’t even count the unacceptable levels of military deaths. I’m not blaming Elizabeth, but there are times people died because of her lack of experience in tactical situations. Because she wanted to negotiate and think rather than act. Partly because she doesn’t have the experience to know how to act.”

Rodney held up a hand, needing to think things through for a second. It didn’t take him long to see Sheppard’s point of view. “Okay, I see what you mean, and I agree. So what’s the issue.”

“I talked to Landry about who would be coming with us as head of the military.”

“Wouldn’t that be you? It has been since Sumner died, and you did great.”

“I’m a major and this type of command needs at least a lieutenant colonel. Colonel would probably be better. But Weir wants me. I have to think it’s because she thinks she can control me. When Landry pointed out to her that I could be XO but didn’t have the rank for CO, that they planned to give it to Caldwell, she apparently made it clear that I would be promoted and remain in command of the military, and that she could guarantee their cooperation based on her contacts in the IOA.”

“She’s strong arming Landry into promoting you?” On the one hand, Rodney agreed that John should be promoted, but he didn’t have great feelings about the way she was going about it. It felt like it tarnished John’s accomplishments in Pegasus.

“Yes, though that seemed to bother Landry less than my assertion that she shouldn’t be in charge.”


Exactly. I told him that I’d certainly accept the promotion and return to Atlantis but not with Elizabeth as the leader of the expedition. That she was valuable as a diplomat and handling the civilian side of things, but that the threat the wraith present warrants a military command.”

Rodney frowned, trying to process everything. He normally processed very quickly, but military issues were alien to him, so he had to think through it in a more linear fashion. “I’m confused. Why would Landry have a problem with that? It seems reasonable, appropriate even, and it’s in line with the charter, not to mention that Landry is military.”

“I don’t know why he has a problem. He said I needed to keep my mouth shut if I wanted to even retain the rank I had, and that biting the hand that was protecting me was a foolish stunt.”

“Wow. Dickish much?”

Sheppard snorted then rubbed his hands over his face. “I don’t know what to do. I feel strongly that this is the wrong thing, but I also hate the idea of everyone—you—being out there without me. But I’m tired of being told to shut up and take it.”

“So you’re going to resign?”

“I don’t know yet. But it’s a possibility. If I fight Landry and lose, my career is over. If I find Landry and win, might career might still be over.”

“I…don’t get that.”

“It’s just the way the military looks at things. If I persuade anyone that Atlantis needs to be under military command, there’s no saying the new CO would even want me to go with him. Look at Sumner and Everett. Neither wanted me around. A new CO might see me as a troublemaker. Or, worse, that Sumner and Everett both died on my watch.”

“Neither were your fault,” Rodney bit out. “And you changed both their minds, so you could change the mind of their replacement too.”

“Maybe, assuming I even got to go. Because making waves for the general of Stargate Command isn’t going to make them look favorably on me even if they think I did the right thing. And if they leave me here, no one is going to put me in a real command again. It’ll be just like after Afghanistan and back to shuttling around generals in some backwater place. I’ve been through too much in the last year to go back to that.”

“And the other option is that you back off?”

“Yes, but how can I do that in good conscience? I feel it’s putting everyone in more danger to keep doing things the way we did them. We need to push for a bigger military force, more munitions and ordnance, and someone with more tactical experience at the helm.”

“But we’re safer with you there.”

“Maybe.” John sighed. “I just don’t know what to do.”

“But not decided yet?”

“No, I’m not decided. I don’t see how I can do what they want, but I don’t see how I can not do it.”

“Just give it a few days, okay? We’re going to have leave soon—these debriefs can’t go on forever. At least don’t make up your mind until you’ve had some time out of this place to think about it.”


And that would give Rodney some time to do what he could.

– – – –

Getting into the Pentagon was a fucking nightmare, but he patiently—for him anyway—dealt with the forms and bureaucracy and the damn waiting.

Finally, he was in O’Neill’s reception area and just waiting for the asshole-in-chief to deign to see him. Rodney had a damn appointment, but O’Neill seemed happy enough to make him wait.

“The general will see you now,” the aide gestured to the door.

Rodney entered O’Neill’s office and found the man himself leaning back in his chair and practically smirking.


His eyes narrowed at the lack of title. “O’Neill,” he shot back.

O’Neill cocked a brow. “Something I can do for you?”

Rodney had been planning to play nice, but that really wasn’t him. He’d decided he wasn’t going back to Atlantis without John, and that was that. So he had nothing to lose by giving it to O’Neill with both barrels.

“I get that you don’t like me.”

O’Neill’s eyebrows shot up and he sat straight in his chair. “That’s not—”

“Yeah, it really is. I even get why. I was in an unenviable position, but I can see how you and yours could only see your side of it. I was an outsider and you had no reason to even try to see my side of things. So you punished me by sending me to Siberia.”

“It wasn’t a punishment.

“Yes it was. And I accepted it because I was into the SGC for the science, not to make friends.”

“You were under contract. You were sent where you were needed.”

“You should read my contract before you wave it around like a weapon. Because, in point of fact, you violated my contract. Not only mine but the IOA’s agreement with Canada by what you did. But I let it slide because I’m nice that way.”

O’Neill snorted.

“And I really don’t care what you think of it or me. Because here’s the thing, no one knows Ancient tech like I do. No one can work with it the way I can. That’s not ego, no matter what’s going through your head right now, it’s a fucking fact.”

“Is that all, Dr. McKay?” O’Neill said stiffly.

“No, it’s not all. I didn’t come all this way on my first vacation time in more than three years. No, I came here because the SGC is fucking everything up. You’re about the risk losing Sheppard, and not just from Atlantis, but from the whole damn program. And you may not care about that, but I’ve checked into it and no one, not even your venerable self, General, has an Ancient gene like Sheppard. The city loves him.

“Hell, the lights are brighter when he’s in the room. I had to actually write an algorithm to dim the lights slightly when Sheppard is approaching to make sure we don’t have excessive power expenditure due to the city’s enormous crush on him.”

“I don’t know what you’re talking about. Not that it’s any of your business, but Sheppard is considered a high-value asset, and we’re not going to lose him.”

“So you’re going to compel him to stay, then? How indentured-servitude of you.”

“That’s not what I meant,” O’Neill snapped. He braced his hands on the desk and took a deep breath. “No matter what I may think of you personally, you are also considered a high-value asset, so I’d like to understand what the hell is going on.”

“Sheppard submitted a report to Landry about all the utter dangerous bullshit we faced out there, about the threat the wraith pose to us and to Earth. Because the wraith have numbers the Goa’uld could only dream of. He pointed out all the violations of the expedition charter that occurred while we were cut off from Earth. How people lost lives because of Elizabeth Weir’s slow action and inexperience in tactical situations. And he was right on every damn point.

“And for his efforts to protect the people working on the city, he was told to shut up and take it. Not only take it, but pretend to like it. And really, fuck all of you. I’ve done my best to play nicely with the SGC, but you’re all on my shit list.

“I’ve reviewed the IOA’s agreement with my country and you’re all so far outside the lines that they’re not even in sight. And that’s not just me. It’s about all the Canadians on board the city who were put in jeopardy because Elizabeth Weir wouldn’t give up command.

O’Neill held up a hand, and Rodney quieted, giving the man time to think. Finally, the general said, “I never understood why Sheppard didn’t take command of the expedition.”

“Did you not read his report? Because I have. He outlined very clearly that he’d discussed the charter with her after Sumner died, and that the situation we were in warranted emergency protocols. She made it clear he didn’t have the pull with the Marines to make that move, that they would follow her over him. And I don’t know if that was true or not. At the time this happened, John was in charge of the military only by virtue of rank, and I know many of the Marines blamed him for Sumner.”

O’Neill winced. “I never saw that report.”

“Maybe you should figure out why. John eventually won most of them over because he’s a fucking badass, but at the time… Yeah, him fighting Weir could have resulted in more chaos, more loss of life, and, ultimately, fighting for our daily survival was more critical than fighting her. But now that I’ve considered everything and read all the charters and contracts, it’s pretty clear to me, and it should be to you, Mr. Career Military Man, that people died because of her lack of experience. That Sumner might have lived to lead the expedition if Weir hadn’t delayed rescue for so long.”

“And Landry had issue with this?”

“Yes, he did. And now that my eyes have been opened to the problem, I’m not going back without someone more competent in charge, and that person has to respect the scientific process and not try to just herd civilians out of the way like Caldwell wanted to do. That’s not gonna fly.

“You can do better. I’ve sure seen you do it for the folks in Cheyenne Mountain and for the whole populace of Earth, but you don’t seem to be interested in doing it for us. So I’m not putting my neck on the line without someone as invested in my survival as I am in taking care of the city and ensuring the expedition’s success. I’m not going back without Sheppard, but he’s planning to resign.”


“Yes, resign. Why do you think I’m here yelling at you? I don’t enjoy your company that much.”

O’Neill glared.

“Don’t act like that bothers you. It’s disingenuous, and I value your forthrightness if nothing else.”

“That’s practically sweet, McKay.” He held up a hand when Rodney was set to reply. “I’ll look into this. I don’t know that I can actually get the IOA to bend on the subject of Weir, but I’ll try to get the situation fixed as much as possible.”

“Not good enough. Fix it or don’t. Leaving her with tactical command or even the right to veto tactical action is not any kind of compromise. I’m going to brief the IOA representative from Canada. Believe me, you’ll have at least one person on your side. Because from everything I’ve been able to glean from talking to him, the IOA is being given a sanitized version of what’s going on out there.”

O’Neill was back to frowning.

“So start with the cold hard truth. Make them watch a video of a wraith feeding. Hell, show them how big a wraith hive ship is in comparison to our BC-304. And then make sure they know just how many of those enormous ships we think the wraith have, not to mention just how many life-draining energy vampires one ship could deliver to Earth’s doorstep. And then you tell me that they want a diplomat in charge.” Rodney turned around and left.

– – – –

“What did you do?” Sheppard asked from the doorway, leaning against the doorjamb.

“Have a nice vacation?”

“Yeah, it was great. Went surfing. Now, what did you do?”

“I went to see my sister, and then caught a symposium on theoretical physics in Paris.”

“That’s not what I meant.”

“Then I have no idea what you’re talking about.” Rodney looked back at his laptop.

Sheppard came fully into Rodney’s office and closed the door. “Audio surveillance in here?”

“No, only video.”

“Three weeks ago, I tell you I’m thinking about resigning, I come back from vacation to find a promotion waiting for me, hear that Landry is being replaced, and find out that we’ll have a new expedition leader. Still a civilian but he’s former military.”

Rodney blinked. “Interesting compromise.”

“Yeah, it’s one way to appease the IOA’s need to have civilian oversight while satisfying the people on the city that someone with tactical experience is at the helm.”

“Who’d they get?”

“Former admiral named Weppler. Career Navy, but his last decade was in charge of Naval Research Labs, so he’s familiar with the scientific process.”



“What?” He shot John an innocent look.

“What did you do?”

Rodney gave in, knowing he’d never truly hold out against John’s persistence. “I told someone the truth.”

Sheppard’s brow furrowed. “And that’s it?”

“The truth, the whole truth, and nothing but the truth. With a bit of assholery mixed in because I gotta be me.”

John took a seat on a lab stool. “Why?”

“Why do I have to be me? Can you imagine me not being me?” He shuddered. “Horrifying.”

“No, why did you get involved?”

Sighing, Rodney saved his work and closed his laptop. “Because I’m not going back without you. The city needs you.” He hesitated for a few seconds. “And I need you.”

John blinked a few times.

“Try not to get emotional,” Rodney snapped, hating how he felt vulnerable. “I’m allergic to soppiness.”

“Admit it,” John said with a grin. “You love me…can’t live without me.”

Rodney rolled his eyes then waved to the whiteboard. “If you’re going to bother me, at least do some math.”

Still smiling, John hopped up and grabbed a purple marker.

Rodney watched him work, feeling something settle in him. Everything was going to work out.

The End

– – – –

Note: You can answer this prompt if you’d like (and link to us both) and share your link with me but you do not have permission to continue my work on this prompt.


  1. I love this thing you and Keira are doing. I also dig your solution to the problem. It always bothered me how much the show seemed to ignore. But that’s TPTB for you.
    Thank you

  2. Aww such a cute story
    I never really cared for Elizabeth


  4. This is so awesome!!

  5. I love it! Rodney does righteous indignation like no ones business – a full on Rodney rant FTW. The whole didaster that was Elizabeth as leader almost killed the show for me. Thank Thor for fanfiction. Also, there should always be pie in fics posted on pi day – even if it’s just a planned piece of pie. 😉

    Thanks so much!

  6. A righteous McKay is a beautiful McKay! He really laid it down. I loved that the whole relationship between Rodney and John was just on the verge, so he was required to take action for more than a ‘safety-of-the-city’ reason, and that he just went to the top to do it, regardless of any animosity between he and O’Neill. Perfectly snarked. Thanks for sharing it.

  7. So lovely. 🙂

  8. This!
    I have complicated reactions to canon Weir because of pretty much everything your Rodney brings up. Once the Wraith were revealed as a threat Weir should never have been left in charge. But then canon put her in charge of the SGC and negotiating with the Goa’uld instead of, oh, the person who had been there from the start!
    Sorry … My point is this is brilliant and so in-voice for the characters. And I love the Weppler cameo.

  9. Oh, that was loverly. And honestly, Weir was absolute scrap in a crisis. But then again logic, reason and common sense have little to do with the various ‘verses presented to the masses via television and movies. It also annoys the crap out of me that all too often females in charge or at least with influence end up being bitches instead of the badasses they should be (Teyla had such promise but there were multiple times I wanted to drop kick her right in to a wealth hive with Weir and Keller chained to her. I adore Rodney going to bat for John because he needs him. Great stuff here. Great stuff. Thank you.

  10. Gp Rodney, only him. Bravo it’s excellent.

  11. Yes! The whole truth with an added mix of Rodney being himself.

  12. Oh wonderful! I wish you were writing the series when they were filming it, as I would love to see Rodney giving O’Neill both barrels, and I am beyond fascinated by the possibilities of your solution to the Weir bu*****t the writers gave us. Please write more in this scenario!

  13. rodney’s assholery is perfect. thank you.

  14. Totally Rodney and John.

    Well done.


  15. This is great

  16. Nicely done!

  17. Awesome! I love Rodney kicking ass.

  18. Greywolf the Wanderer

    fuck yeah, this is how it shoulda gone!

  19. This is SO good, so smart. I wish the TPTB on the show had been a little more creative and given the set-up a little more thought. They just stream-lined the changeover into 2nd season because it didn’t interest them, they just wanted to get pack to the explosions and the running around.


  20. Rodney’s conversation with Jack gives me life. The snark! The ‘don’t bullshit me I’ve got better things to do’ vibes! Totally love this, thanks for sharing!

  21. Rodney can and will change the universe when motivated…

  22. They say the truth shall set you free. In this case the truth saved their asses, and a whole host of other asses too. I love these two. Love them more when you show off that spine of steel that Rodney keeps hidden under all that snark. 🙂 Thank you for a wonderful read.

  23. Where is Weppler from?! I can’t remember. I know it’s familiar, but I just can’t make the connection.

  24. Great story. Thank you.

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