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The last thing John remembered was exploding. Well, okay, he didn't really remember it, but close enough: one last thought about dying for his people and maybe he really did have a martyr complex, loading the program, and then the light and heat and terrible noise of a dozen dying hives. And then silence.
So the fact that he woke up at all was surprising enough. The fact that he woke up to Rodney sitting at his bedside was downright alarming. "Mmm," he said, licked his lips, tried again. "Mkay?"
Rodney jumped about a foot in the air, and his thousand-yard stare settled on John's face. He looked bad, almost as bad as when he'd been building the nuke: eyes red and shadowed, face even paler than usual, hair sticking up weirdly on one side. He was wearing a uniform jacket, but somehow the patches had been ripped off the sleeves, leaving a boxy halo of broken threads. "Hi, Colonel," Rodney said, a little too brightly. "Glad to see you're awake. Very, very glad. Seriously, you have no idea."
"Why am I alive?" John asked. He certainly felt like he'd exploded, even if was clearly all in one piece and breathing: his muscles felt stiff and sluggish, his skin tight and raw. There were no burns on his hands, though; when he raised them to his face; if anything, his skin looked a little pale.
Rodney smiled, looking kinda demented. "The Daedalus beamed you out at the last second. Again. You were, uh, pretty badly burned, but still in one piece, and now you're awake, which is the important thing. Very important. You need to talk to somebody about this whole martyr complex, you know?"
John shook his head and then waited for the room to stop shaking with it. "The Daedalus was nowhere near the planet."
Rodney's smile got strangely fixed. "Um, no. It wasn't supposed to be."
"What did you do, McKay?"
Rodney took a deep breath and fixed his eyes on a point over John's shoulder. "Well, uh, see, Colonel, while you were running off to blow yourself up—again—you really do need to stop that, by the way, it's making everything horribly awkward—um. It turns out General O'Neill left some kind of standing order, so Elizabeth got recalled to Earth, and there was this thing with the IOA, and, well, it was actually originally Radek's idea, which really shouldn't surprise me because we always knew he had a criminal mind somewhere under all that hair—"
"McKay."
"ZelenkaandLornehijackedtheDaedalus," Rodney blurted.
John took a deep breath. "The who what now?"
"They hijacked the Daedalus," Rodney said again, "and, well, I helped, but that was really mostly their doing, and of course once they did that then we had to deal with the Apollo, which, um, well, that I have to take the blame for—"
"You hijacked a spaceship?" John asked. "And what do you mean, 'deal'?"
"Um," Rodney said, "I mean I wrote a computer virus that ate most of their operating system and blew out their railguns. They're about four AUs out from us and really, really angry."
John shut his eyes and opened them again, but no, either this was real or he was in Hell. "Rodney, why did you sabotage one spaceship and hijack another?"
"I told you, that was Zelenka—"
"Answer me!"
Rodney straightened his back and folded his arms across his chest, eyes wide and bloodshot, but his voice momentarily lost the creaky whine of nerves and exhaustion. "Because they had Elizabeth under house arrest back on Earth pending possible charges of treason and they were going to haul you back for a court martial if you survived and it didn't look like you where going to for a while. They were going to recall the expedition and sink Atlantis and at least half of my staff were never going to work on anything useful again because the IOA are vindictive idiots and they'd rather run away with their tails between their legs than permit the advancement of human thought and...and I was not going to let that happen. Not again. I couldn't."
John took a moment to process this, then valiantly tried to sit up. He realized he wasn't in the infirmary; he was in one of the lower labs, a musty-smelling place they had cleared of cool toys but not actually needed to use. He wasn't in a bed, either, but something that looked an awful lot like a coffin made of smoked glass and embedded with little colored lights. "What the hell is this?" he asked, half-sensing the Ancient interface inside it.
"Oh, it's a healing device," Rodney said. "That's, um, that's how you aren't dead. It doubles as a stasis pod, which is how we were able to hide you from the Apollo's scanners while they were, um, trying to invade."
"They tried to—"
"Not invade. Invade was a bad worse. Um. Visit with extreme prejudice? Don't worry, we fought them off," Rodney smiled. "Nobody even died. I think. Unless you count whales."
"What, whales—?"
"And we got Elizabeth back," Rodney said, almost hysterical now, "although I don't think General O'Neill is ever going to speak to me again, and I've basically committed planetary treason now, and Jeannie's going to think I just did it to get out of Thanksgiving tofurky. Um. Did I mention the part where we can't go back to Earth?"
"I kinda figured," John said. "How'd you get Elizabeth back if the IOA had her?"
"Um. Hostage exchange."
"Hostage—?"
"The personnel who wouldn't help us," Rodney said, "I had just confined them to quarters while we moved the city—"
"You moved—"
"—but I told Woolsey I wouldn't send them home unless we got Elizabeth back. I threatened to ask for Tok'ra arbitration. You can't just detain a foreign head of state like that."
John rubbed his eyes and sat up fully in the pod thingy. "Rodney, Elizabeth is not a head of state."
"Honestly, Colonel, have you not been paying attention?" Rodney said. "She's our governor. We've seceded."
"You seceded us?"
"There was a vote!" Rodney's radio squawked, and he prodded at it before standing up. "Come on. The Apollo is sending us threatening messages again, and Lorne wants to know what to do with the Satedans, and apparently Simpson is writing erotic couplets into the constitution, and we really, really, need you now."
John said, "Huh?"
Rodney smiled the crazy smile again. "Come on, Colonel. You're the military commander of the Republic of Atlantis. Can't be seen lying around on the job."
John levered himself out of the pod even as he said, "McKay, I blew myself up today and woke up in a revolution."
"Last week, technically. You blew yourself up last week. You just haven't been stable enough to wake up until now."
"So what have you been—" John shook his head. "Never mind. I don't want to know."
"I'll explain it all after coffee." Rodney stopped short in the hallway. "Oh my god. I cut off diplomatic ties with our only source of coffee, didn't I?"
"You think of that now?"
"Fog of war and all, Colonel. I'm not exactly a career subversive." Rodney shook his head. "Well. We'll figure something out. Did I mention we have two ZPMs now?"
"No," John said, "and if you stole them from the US Air Force, I don't want to know about it."
"Nonono," Rodney said. "Not stealing. Stealing is wrong. We, um, traded for them."
"Traded what?"
"Caldwell," Rodney said quietly.
"McKay!"
"What? He's an enemy of the state and we needed to power the shield somehow!"
They stepped into a transporter and Rodney mashed a button for the central tower. John realized he was still in his smoke-scented, slightly bloodied uniform from the suicide run; he tried to make it look a little more military-commander-of-rebel-outpost-y. "What's Elizabeth think of all this?" he asked Rodney as they stepped into another corridor.
Rodney flinched. "Um. That's actually part of why I'm so glad to see you awake."
"You didn't take Elizabeth hostage, did you?"
"What? No!" Rodney looked at him like he was insane. "Elizabeth isn't a hostage. She's just, um, on a lot of really good drugs right now, and whenever I try to ask her opinion on something she smiles really big and starts singing. In Ancient."
"What? What happened to her?"
"Hostage exchange didn't exactly go smoothly," Rodney muttered. "But the point is, she's going to get better, and you've gotten better, and now you can take over negotiations with the Genii."
"With the—why are we negotiating with the Genii?"
"Oh, you know, food, bullets, nuclear weapons, the usual. We promised them some of what Elizabeth's having. They're really very lovely people if you can ignore the paranoid authoritarianism and the fact that they glow in the dark."
John was quiet for a moment, then: "Rodney, when was the last time you had any sleep?"
Rodney just grinned at him. "That's what you're here for, Colonel. Or should I call you General now? You could really make up any sort of rank you wanted, now, I suppose, though it'll take some getting used to and I suspect it'll give Ellis an aneurysm."
"I'll think about it," John said. "Can I at least change clothes before I take over my diplomatic duties?"
"Oh, um, maybe. But first there's Ellis and Woolsey and the Genii and Simpson and—well—Chuck has a list. He'll explain it to you. He's very good with lists."
They stepped into the control room, which had a few more bullet holes and blast scars than John remembered, but was bustling with people. They were poking things and shouting at each other and passing tablets and laptops around like footballs, a perfectly ordinary scene except when you noticed that all of them had torn the flags off their uniforms and they kept shooting nervous glances at the gate. Ronon was standing guard down there, and John thought if he could get used to seeing Ronon in a uniform jacket ("Lorne says just treat him like a warrant officer, whatever that is," Rodney muttered, "It's a long story, um, but he's got a platoon of crazy people on his side and they do a really disturbing salute and we kind of need them,") he could get used to anything.
Chuck bounced up to them with a crazy exhausted grin to match Rodney's and a very long list on a tablet. "Good to see you up and around, sir," he said to John.
"I'll let you know when it's good to be up and around," John said. People were staring at him, and he took a deep breath, pushing down thoughts about revolutions and invasions and treason. He'd been ready to turn his back on Earth before, had as good as done so when he went through the gate to take out the armada. He'd just never expected all of Atlantis to come with him.
Now he had to a job he'd never trained for with limited resources and no option of retreat. He just hoped he still remembered how.
"Sir?" Chuck said warily.
John smiled at him. "Right here, Sergeant. Tell me what we've got."