Thanks once again to those who have reviewed -- I greatly appreciate it, even those that are a bit ... uncertain about the direction that this is taking. I can sympathize with those who are having a hard time with the AU versions of the characters. One of the problems with starting at "Trinity" is that Doranda really isn't where things started going wrong here; it was around the time of the Siege. But I didn't really want to put my readers through a retelling of the episodes leading up to this, since "Trinity" is where events really started to blatantly diverge. The basic events of the preceding months were pretty similar to how they happened in the show, just with more distance between the main bunch.

Anyway, at the risk of giving away spoilers, I swear it doesn't stay this depressing forever!

Chapter Three: Vigils

Being off Sheppard's team turned out to be a tremendous relief, although technically, McKay knew that he wasn't really off, yet ... not until he talked to Sheppard, which he kept putting off. No offworld assignments had come down the line yet, which was interesting -- he knew he should ask Elizabeth about that, but he didn't really want to talk to her at the moment, either. Maybe Radek had dropped a word with her about the importance of their current project, so she'd had the team stand down. Or something. He didn't know and didn't care. Arcturus was consuming all his waking time, to the point that he completely forgot to ask Carson what that meeting with Weir had been about. Actually, he hadn't seen Carson in days -- probably the doctor had lab work of his own to keep him busy, if that Wraith thing had panned out at all. One of these days he'd need to ask, but right now, he was living, breathing and sleeping Arcturus.

The "bridge" idea sounded simple, and on its most basic level, it was. But like so many simple things, implementation was turning out to be a bugger. McKay figured that months of work still lay ahead of them. But all he needed was to know if the damn thing would work, so that he could give that information to Caldwell to take back to Earth.

Of course, people still kept interrupting him for stupid problems that they could have figured out in five seconds if they'd just used their brains for thinking rather than calling the labs in search of a head scientist who had better things to do. One of these problems -- a simple short in a power coupling that was causing erratic equipment malfunctions -- took him up to the gateroom; it was the first time he'd been out of the immediate area of the labs in days. Oblivious though he might be, he couldn't help noticing the extra-heavy guard on the gateroom -- there were armed soldiers standing at attention everywhere, it seemed. Straightening up from the malfunctioning console after fixing it, he asked Chuck, "Are we expecting an attack, or something?"

"What?" the tech asked in confusion, then followed McKay's eyes to the extra guards. "Oh, no, sir. That's standard now that Colonel Caldwell's in charge. He thought our gateroom security was too light before."

McKay had stopped listening at "Caldwell's in charge." What the hell? Had he fallen asleep and woken up in the Twilight Zone? He tapped his radio. "Elizabeth! Sheppard!"

Weir's voice answered. She sounded exhausted. "Rodney, this had better be important."

"What the heck is this crap about Caldwell being in charge of the military? Is this someone's idea of a joke?"

There was a long, dead silence. Then Carson's voice broke in, "Rodney, I'd like to see you in the infirmary before you embarrass yourself further."

"Not now, Carson. I want to talk to Elizabeth."

"She's down here already, Rodney. That's where most of us are. Now move your stubborn arse, would you?"

------

"Sheppard's turning into a bug and nobody told me?"

He'd run to the infirmary, flat out, with all kinds of horrible scenarios spinning through his mind: a disease spreading through Atlantis, a terrible accident offworld ... but the truth had turned out to be both a huge relief and just about the most disturbing thing he'd ever heard.

In fact, he thought at first it was a joke; it had to be a joke. Even for the Pegasus Galaxy, this was a little too crazy. But the grimness in Carson's eyes, the fine lines of exhaustion in his face ... and the tension in the others around them, in Elizabeth and Teyla and Ronon and Carson's staff ... all let him know that something was terribly wrong.

And he had been the last to know.

He couldn't figure out whether to be angry at himself, or at them.

"Where is he now?"

"He's in his quarters, under guard." Carson leaned against a countertop, and rubbed his hand across his face, where a light spray of stubble was beginning to show.

"What -- you're holding him prisoner?" McKay just couldn't wrap his mind around this. It was too much.

"He still has free run of Atlantis," Elizabeth said, stepping forward. "But he's to be kept under guard at all times. We have no idea to what extent this is affecting his mind, as well as his body."

"Well, you're going to stop it, right?" McKay turned to Carson. "You can fix it, right?"

Carson sighed. There was a look on his face that McKay hadn't seen since Hoff; he looked tired and, disturbingly, old. "That's what we're trying to do, Rodney. Actually, I'd like to bring your science team in on this. The medical staff is coming up with nothing, and there might be something in the Ancient database that could help."

"Yes, yes, of course. Why the hell didn't you ask me sooner?" He still couldn't believe they'd left him out of the loop.

Carson's grip on the edge of the countertop tightened. "We didn't really know the extent of the problem until just a few hours ago. At this point, it looks like he's got -- days, no more."

"What do you mean, 'he's got days'? Days until what?"

"Rodney --" Elizabeth began, sounding impatient.

"He knows what I mean, Elizabeth," Carson interrupted her, in a soft and apologetic tone. "You do, don't you, Rodney? In a few days, whatever makes him John Sheppard -- it's going to be gone."

"You mean he'll be dead." Dead was bad, but ... he could almost cope with dead. If he didn't think about it too much.

"Eventually," Carson said, which wasn't comforting at all.

McKay was aware that everyone seemed to be watching him expectantly. He could feel the weight of Teyla and Ronon's stares in particular -- and he wondered if Elizabeth had told them that he'd asked to quit the team yet, until realizing that no, of course she hadn't; she was waiting until he talked to Sheppard. Who was currently mutating into a bug ... Wraith ... thing.

"So," he said, rubbing his hands together with a confidence he didn't feel. "You guys have a plan yet?"

------

The idea of bringing back Iratus eggs was completely insane. A plan only Carson could love. Unfortunately, it was also the only thing they -- and Sheppard -- had.

McKay didn't go along, of course. There would be no possible way that he could help; he'd only get underfoot and make it harder for the military-types and Carson to do their jobs. Not that he'd put it in those terms, of course. Clearly, he was much more useful here on Atlantis, searching the database for any hint that the Ancients had had to deal with this sort of thing before.

There was no reason to go, every reason to stay. So why did it feel so wrong, that his team were out there risking their lives to save Sheppard's, while he sat in a safe, comfortable lab?

They weren't his team anymore, he reminded himself, sitting back and rubbing at his sore eyes. They were just ... people, with whom he had once ... traveled ... places. Yeah.

Looking up from his computer, he jumped to see a figure standing in the doorway. Sheppard. At least, he thought it was Sheppard; it wore a hooded sweatshirt emblazoned with the USAF logo, the hood pulled so far forward that only a pointed chin was visible. A burly Marine hovered in the corridor just outside.

"Colonel?"

Sheppard pushed back the hood just a little. His face was turned, so that McKay could only see one side of it. What he could see looked normal, though. Maybe Carson was exaggerating the severity of the problem.

"Looking for Beckett," Sheppard said. There was something a little ... off about his voice. It was too rapid, with an unusual throatiness to it.

"He's offworld, hunting Easter eggs." And there it was again, that flicker of guilt that he couldn't quite deny.

"Oh. Right." Sheppard ducked his head away, an oddly diffident gesture from the normally confident pilot. "I didn't realize that he -- I mean, I knew Teyla and Ronon were, but Carson -- I wasn't expecting that."

Sheppard didn't ask why McKay wasn't out there, egg-hunting with the rest of them, and in a way that was even worse. Guilt rose up and nearly choked him. Perhaps that was why he blurted it out, the thing he hadn't meant to mention: "I quit the team."

"What?" Sheppard's head came up, the hood falling back, and Rodney blanched from the scaly blue skin that was revealed. He didn't mean to; he just couldn't control his reaction. He saw Sheppard's face flicker at that, becoming harder, as the Colonel reached up to raise the hood again, and looked away.

"Well." Sheppard sounded almost amused. "It's a pointless gesture, Rodney; without me, there's not exactly a team anymore, is there?"

The grim fatalism pissed off McKay: as if they weren't doing everything in their power to find a cure, as if they wouldn't find a cure at all. As if Sheppard could just discuss his own demise in that flippant tone -- it was stupid, idiotic ... and nothing made him angrier than blatant stupidity, especially from someone who he knew wasn't stupid at all. "It was before that," he snapped. "I turned in my resignation to Elizabeth days ago. And she approved it. Just said I had to talk to you before it'd be official. So -- here I am, talking to you."

"Oh," was all Sheppard said, and that single little word made McKay even angrier. The very least that Sheppard could do was have the decency to ask questions. Or maybe fight back. It felt too much like kicking him while he was down, doing this now. And yet his mouth just kept motoring on.

"Yes, 'oh', Colonel. And Elizabeth told me that you asked to have me removed from the team already --" oops, maybe that had been in confidence, but it was too late now "-- so I figured you'd be pleased. There just hasn't really been a good time to tell you."

"No ... I suppose that's true."

The silence stretched uncomfortably between them. The worst part, McKay thought, wasn't the anger. There wasn't really a lot of anger in this, not as much as there should have been, and that was the worst part of it all. A strong friendship, like the one they'd once had, could survive rage. What it couldn't survive was indifference, and that was what it had become.

He stared at Sheppard and realized that he was looking at a stranger. Not because of the blue scales; he didn't really care about that. Well, all right, he did care about it, because it was creepy and weird and also, it was killing Sheppard. But above and beyond that ... he didn't really know the man standing across the room from him. He'd known him once, known him well. But they didn't know each other anymore.

"When Carson comes back, I'll be in my quarters," Sheppard mumbled, and turned away. It was only after he'd vanished from sight that McKay realized Sheppard had probably thought he'd been staring at the blue scales on his face and neck.

"Rodney, you ass." He buried his face in his hands, briefly, then turned back the database with his shoulders resolutely squared.

------

"I put him in a medically-induced coma for now. I was afraid he might break through the restraints."

Behind the curtain and the Marines guarding it, Carson's voice was faintly audible. Lorne smiled apologetically at McKay and spoke, obscuring whatever Caldwell said in response. "I'm sorry, Doc. Colonel Caldwell's orders -- everyone has to leave."

McKay jerked his head at the curtain, belligerent and stubborn and not even sure why, except that anger gave him something to cling to. He hadn't spoken to Sheppard since telling him of his decision to leave. "I'm not trying to stay. I just want to know why they stayed."

"Colonel's orders," Lorne repeated, his eyes sympathetic, but implacable. Behind the curtain, Elizabeth's voice could be heard, asking quietly: "So what now?"

McKay turned on his heel and left. He strode past Teyla and Ronon, hovering in the corridor, forming their own little circle of grief and fear. Once, he might have been a part of that, but he could tell that theirs was a private sort of sorrow. There was no deliberate effort to exclude him, and Teyla gave him a sympathetic look as he passed, but he could sense that this was a place where only Sheppard's friends were welcome -- and he wasn't one of them.

Didn't want to be one of them.

He'd always had a bit of contempt for people who hovered around hospitals hanging over their comatose loved ones -- unconscious people didn't require moral support, it was that simple, and if you really were too upset to do anything useful, the very least you could do was wait at home rather than hanging around the hospital getting in the way. Knowing that he himself had done that exact thing in the past -- after Sheppard's first bug incident, for example -- only made him more irritated, both with himself and with irrational idiots who thought that the infirmary staff wanted them underfoot. Teyla and Ronon ... fools, both of them.

He went back to his quarters and took a long shower, just standing under the water with his face upturned, trying to wash away the mental image of Sheppard writhing against the restraints. It was a lousy way to die, and even if he'd never given a damn about the man, he wouldn't have wanted to see someone die that way. It was worse, far worse, to see those wild, hate-filled yellow eyes in the barely-recognizable face of someone he'd once ... known. He still felt guilty for not having gone along on the Iratus bug egg-hunt. There was no reason why he should have, and he knew it. But still.

Standing under the warm, cleansing cascade, he found himself thinking of his mother -- it had been years since he'd dwelled on that. He was surprised at how much power the lingering grief still had over him. They'd been enemies when she died, his mother and himself; it had been years since they'd spoken, divided by too many cutting remarks, too many little betrayals and cruelties. He had come to visit her, though, in the final days of her cancer, even after promising himself that he wouldn't. He still felt sick with the memory of how he'd stood in the doorway of her hospital room, trying and failing to see the strong, abrasive woman he'd once known in the pale shadow that trembled in the hospital bed. He hadn't spoken to her, and she'd died, days later, without ever knowing that he had come.

The rifts had been too deep to mend, he had decided; all he could have achieved by trying to bridge them was to have one final fight with a dying woman.

Deathbed reconciliations might play out fine in the movies, but in Rodney's experience, it was just one more thing that didn't work out in the real world.

He stepped out of the shower when he started to shiver, and was toweling himself off when his radio crackled on the bedside table.

"Rodney? It's Elizabeth." She sounded breathless, excited. "I'm sorry to wake you. I know it's late. But Carson has an idea that he thinks could help Sheppard's condition."

He froze with one hand holding the towel and the other holding his radio against his ear, unable to suppress a sudden, quick smile or the hopeful "Really?" that her words startled out of him. Getting himself back under control, and reminding himself that whatever they'd come up with was exceedingly unlikely to work, he added, "Don't tell me that you're letting Carson play at science again."

"Just come up to my office, Rodney, please. Weir out."

He stood for a moment, just staring at the radio in his hand, heart beating fast and not quite sure what he was feeling.

------

Two weeks.

Long time to avoid the infirmary.

He'd been busy, though. He'd had a report on Caldwell's desk before the Daedalus had left for Earth, and in between the usual minor crises, he and Zelenka had been working on the plans for the bridge.

McKay was pretty sure that, after another trip back to check their plans against the existing equipment on Doranda, they'd be ready to start building the thing. He was especially proud of having managed to modify their "best case scenario" design into something that could be done with the materials available on Atlantis and Doranda.

He had waited until after the Daedalus had broken orbit to give his report to Elizabeth -- because he was still afraid that she'd try to go over his head, try to stop him. With the report already winging its way towards Earth through hyperspace, he hoped that she'd be too concerned about presenting a united front to the oversight committee and the SGC to try and pull rank on him through the Stargate. So far, this seemed to be correct.

He might be getting better at this whole manipulating-people thing, because he thought he'd found the string to pull in order to get Elizabeth to cooperate with his plans for Project Arcturus. She was afraid of losing Atlantis to the military. He hadn't realized the depth of it, until he'd gone to Caldwell to get the Arcturus project re-opened. He also hadn't realized how tenuous her control of Atlantis had really become until the last couple of weeks. Sheppard's people had never been more than nominally under her control, but with Sheppard in the infirmary, he'd noticed that the military had pretty much been doing their own thing in "their" areas of Atlantis. No one saluted when Elizabeth walked into a room; no one stood up. Sheppard would probably try to put a stop to that once he was back in charge, but there was only so much he could do to reign in the runaway train of public sentiment.

Elizabeth Weir was very much a woman walking a razor's edge. Her control was slipping; Atlantis was fragmenting. And McKay, well ... he felt like an absolute louse for using it against her, but he told himself that the Arcturus project made it worth a little bit of harmless -- well, it wasn't even manipulation, was it? Just nudging. This project was bigger than any of them. When history judged them, the benefits of their work would far outweigh any minor damage that had been caused along the way.

They had to make this work. For Earth, for the Pegasus Galaxy and the war against the Wraith ... for all of them.

"Dr. McKay?"

His head snapped up from his computer screen. He'd been drifting, staring at a screensaver. He was tired. Hadn't been sleeping well. Too much working. Too much thinking.

Teyla stepped cautiously into the lab. She wasn't comfortable here; her usual grace and composure did not hide her obvious tension as she carefully avoided the busy lab techs and the unfamiliar equipment.

McKay tried to recall if he'd ever seen her in the labs before, and drew a blank.

"Teyla?"

She smiled at him, but it seemed strained. "Colonel Sheppard was released from the infirmary today."

"Oh, was he?" Damn. Avoiding the infirmary was relatively easy, although it did mean that he only saw Carson in passing in the cafeteria. Now he'd have no idea where Sheppard might turn up next.

"He appears to be doing well." Teyla looked away from him, uncomfortable in a way that he hadn't seen on her before. "He told me that you have resigned from the team."

Oh, damn. With everything that had been going on, he had completely forgotten that Teyla and Ronon didn't know. "I was going to tell you," he said, wondering if he sounded as lame as he felt.

The strained smile was back in place. "I know that you would have."

"It's just -- I'm needed here, you know, and it doesn't make sense to send the head scientist and Atlantis's chief military officer offworld on the same team ... You understand, right?"

"I understand, yes," she said.

To his dismay, there was hurt in her brown eyes -- of all the things he'd been expecting, that hadn't been one of them, and somehow, it cut him to the quick. He wanted to tell her that it wasn't her fault, but, as usual, the words weren't right.

"You'll need another scientist, of course. I mean, now that I'm gone. I was -- I'm thinking Zelenka. He's been reluctant to go offworld, and maybe this is just the opportunity that he needs. You know, to build up his confidence and all --"

He talked faster as she slipped towards the door, smiling an apologetic yet final goodbye.

"Yes," she said as he paused for breath, "Zelenka seems intelligent and competent. He will not be you, though, Rodney."

She was gone before he could respond to this -- before he could even consider it. He had hoped that they would miss him, of course. But somehow, he hadn't really expected it, and for an instant he couldn't breathe.

For an instant he wondered if he was making the right decision.

Clenching his teeth, he spun around on the lab stool and began swiftly typing on his computer. An email, very short, addressed to Sheppard. You'll need a scientist for your team. How about Radek?

To his surprise, the answer came back almost immediately. One word.

Fine.

Just that.

McKay tried to tell himself that he'd won that round. Inexplicably, it felt more like losing.

----

TBC

Next chapter: The actual plot begins to emerge...