Author's Note: This is a new WIP, and it will be fairly long. At this point, it's about half written, but still undergoing revisions.

This story will contain spoilers up to Season 3's SUNDAY. This is also a little darker and heavier than what I normally write, though not without its share of friendship moments (hard as that may be to believe from the first chapter).

Title: The Light of a Fading Sun
Rating: A fairly strong T/PG13
Spoilers: This is an AU version of events diverging around the Siege. It contains heavy plot spoilers through Season 3's "Sunday".
Summary: Perhaps the only thing worse than blowing up 5/6 of a solar system is not blowing it up at all. Following the Siege, the characters drift apart ... but in their AU universe, the events on Doranda will have far-reaching and unexpected consequences. And theirs may not be the only universe affected.

Note the First: Thanks to Kodiak and Tazmy for their invaluable beta help, particularly on the obnoxiously stubborn first chapter. I bet you guys had forgotten about this one, eh? But I'm still working on it!

Note the Second: I wanted to thank everyone for their wonderful, wonderful story reviews. I'm still really lousy at replying to reviews here (I do better on LJ for some reason) and I apologize for that, but I read every one. Thank you all so much for reviewing my stories!

The briefing hadn't gone well. But then, he hadn't expected that it would.

No, Elizabeth had said. You can run all the simulations that you want, but I've made my decision. The answer's no.

The only light in the hallway was the soft glow of the ever-present bubbling pillars, and a few strips of dim track lighting to keep people from walking into walls. He passed a young lab tech lost in examination of one of the pillars -- she was one of the new people in Hydrology, fresh off the Daedalus. He didn't acknowledge her; she didn't even see him.

They could have powered the whole place effortlessly. Never had to worry about storms or depleted ZPMs or Wraith, ever again. The solution was in the palm of his hand -- the answers to the calculations that even the Ancients couldn't solve. And no one would listen to him.

The answer's no.

Sheppard had sat in on the meeting, at Elizabeth's request. Rodney wasn't sure why. The Colonel had not been back to Doranda since the initial survey. Had not been there for the test firing ... for Collins' death.

A small knot of Marines walked past him. They started laughing after they went by. He'd caught some sideways glances, not particularly friendly, and wondered if they were talking about him behind his back.

He wasn't sure whether it bothered him that they might be. He had little but contempt for the military in the city. The new people weren't the same, and the old ones had ... changed.

They'd all changed.

He wandered by one of the darkened rec rooms. A quick and unexpected flash of memory caught him -- lounging on a couch with his laptop, nitpicking the special effects in some inane B-movie, while Sheppard threw popcorn at him and Ford laughed and Teyla tried to mediate between the three of them.

But these days, the place was military-only. It didn't have a "CIVILIANS NOT ALLOWED" sign, but everyone knew. The scientists had their own areas of the city; the military had others. There wasn't any overt hostility if someone strayed into the wrong lounge or the wrong side of the cafeteria -- just cool stares and a general cessation of conversation.

It seemed like a very long time ago when they'd all been in this together.

In those days, the team movie nights had been an imposition on his work-time, deeply resented. But still, Sheppard or Ford had come down to the labs on a regular basis and rousted him from some vital-to-the-safety-of-the-city project in order to drag him off to see an inane movie that he'd seen a hundred times. He'd never stopped complaining, and yet they'd never stopped coming to find him.

So many were gone -- so many dead.

Ford. Grodin. All the many casualties of the Wraith siege and before.

Collins.

He left the rec room behind with barely a twinge. The memories that it represented belonged to a different time in his life -- before the Wraith siege, before the deaths, before Everett and the Daedalus arrived to disrupt their tight, insular little world. Going through the gate, going out with Sheppard's team, was work these days. It was something he did because it was his job, not because he enjoyed it. His real life was in the labs. He'd considered, several times, turning in a request to Elizabeth to be taken off the team. It had never made much sense sending the head of the science department offworld. He wasn't sure what kept him going -- stubbornness, a sense of duty, an unwillingness to let go of the past.

His wandering steps turned in the direction of the cafeteria, hoping it would be deserted at this time of night. Though it was dim and quiet, a little group of scientists sat near one wall, papers spread on the table in front of them. He recognized Radek among them, and was briefly tempted to go over and join them, to lose himself in a discussion of theoretical energy physics.

But any discussion among the scientists tonight would no doubt turn to Collins' death, and he couldn't ... deal with that right now. Not when the answers that could have saved Collins' life were staring him in the face, and Elizabeth wasn't willing to listen to him.

Another brick in the wall ...

McKay took a muffin, and retreated without being seen, to continue on his silent tour of the sleeping city. For a moment, he considered going down to the workout room to see if Teyla was still up, before remembering that she was offworld at the moment with Ronon the Barbarian. She wasn't all that useful for bouncing off ideas, and she couldn't possibly have the slightest comprehension of the strategic importance of Doranda ... but she was comforting to be around. He told himself it didn't matter, but that didn't necessarily make it true.

He still got along with Teyla. He wouldn't say that they were friends, exactly -- but then, he knew, they never had been, and maybe that was why he still got along with her now. They had nothing in common, and the growing strain between the teammates only served to cast their differences into sharper relief. But Teyla smiled at him when he happened to see her in the cafeteria, and that was nice. They weren't the sort of buddies who went out of their way to sit together at lunch or hang out after work. But with everything else falling apart, they still managed to be amiable co-workers.

Tonight, though, Teyla was off somewhere with the caveman, and he felt an unexpected pang that bordered on betrayal.

Still a sore point ... Ronon. Of all the people Sheppard could have picked to replace Ford -- why him?

McKay hadn't even known that Sheppard had (inexplicably) invited Ronon to be on the team until they'd all shown up for their first mission together. That had been -- awkward. The first thing Rodney had done after they got back was storm up to Weir's office to lodge a complaint. Elizabeth had listened to him rant and then leaned forward and said softly, "Rodney, John's your team leader. The decision about who goes on your team is his, not yours. And I approved it."

"Yes, but damn it, Elizabeth! He invited a freaking barbarian and didn't even ask the rest of us!"

"It's not your call, Rodney. I'm inclined to agree with you that John ... could have handled the situation a little better, but I'm not going to second-guess the way he handles his team. I approved his selection of Ronon for the team, so if you want to be angry at someone, I'm as much of a target as John."

McKay rocked back on his heels, caught between anger and a sharp, unexpected hurt as the meaning of her words sunk in. "You knew and you didn't tell me?"

Elizabeth sighed. She looked suddenly very, very tired. "I told you, Rodney: I won't second-guess John's decisions when it comes to his team. I'll have a talk with him about openness and communication within the team, but ultimately, I'm not going to micromanage him. Do you think you can accept that?"

As if he had a choice.

Of course the entire gateroom -- including the rest of Sheppard's team -- had heard his tirade. McKay wondered if it was just his imagination that Ronon loomed in a somewhat more threatening way at the post-mission debriefing. For his part, Rodney was determined to cut the caveman not an inch of slack. So Sheppard intended to replace Ford with someone who didn't even understand basic hygiene, did he? That was just fine, but McKay didn't have to talk to him.

Luckily not talking to Ronon had proven astonishingly easy. The only time they ever saw each other was during their missions, and since Ronon spoke approximately one word per hour, conversation with him wasn't a huge threat. On Atlantis, Ronon's life intersected McKay's to an even lesser degree than Teyla's did.

And Sheppard, well -- the less said of Sheppard, the better.

Sheppard. Hmm ... maybe ... McKay slowed, stopped, and stood in the corridor, eating his muffin and thinking.

Elizabeth trusted Sheppard. She listened to him. Not as much as she once had, but then, none of them ... but that train of thought was going nowhere.

Maybe he could get Sheppard to talk to her -- intercede on his behalf.

He walked briskly towards Sheppard's quarters before he could lose his nerve, running over possible scenarios in his mind. If this didn't work, he could always go to Caldwell, go over Elizabeth's head and play the military card. The idea gave him a cold satisfaction that somehow left a bitter taste in his throat.

This is important, McKay, he told himself. More important than you or Elizabeth ... or Sheppard ... and a hell of a lot more important than your squeamishness about doing what needs to be done.

He paused outside Sheppard's door. For a tempting instant he thought about just skipping Sheppard and going straight to Caldwell. He hated to think of the amount of interference he'd have to endure if the military got hold of the project, but they could definitely trump Elizabeth.

He had a feeling, though, that if he did that, it would be the final nail in the coffin of his good relations with Atlantis's civilian leader.

And if Sheppard ever finds out you're using him, you'll be lucky if he doesn't just shoot you.

He wished he could just ask. There had been a time when Sheppard really might have gone to bat with Elizabeth for him. Now, though ... now he couldn't even think what arguments he might use. In fact, he had no idea how much Sheppard actually knew about the whole Arcturus situation.

After the initial survey when they'd discovered the Ancient installation, Sheppard hadn't been back to Doranda -- Lorne's team had been sent along instead, to help the scientists explore the facility. Heaven knew what he'd been doing instead; paperwork, maybe, or training recruits. It was pretty clear that the thrill of discovery wasn't a big issue for Sheppard, not these days; ever since Ford, the man had pulled back, retreated into his G.I. Joe persona. He was a lot more conscientious about his duties than he'd ever been, as if he had come to the conclusion that all the deaths over that first year could have been prevented if only he'd dotted another i, crossed another t. It was a much more detail-oriented John Sheppard who ran the Atlantis military these days -- a lot more responsible, a lot more mature, and one hell of a lot less fun. McKay never would have guessed that he'd miss the irresponsible, annoying version of Sheppard, but he couldn't imagine the more adult Sheppard ever throwing him off an Atlantis balcony or wanting to explore an alien hatch.

This would be the first time they'd actually talked to each other, one-on-one, in ... months, perhaps.

If he gave himself another minute to think, he was going to walk away.

McKay screwed up his courage and knocked on the door.

There was a long silence, and Rodney realized, belatedly, that waking up a person to get a favor out of them was probably not the world's greatest strategy. Especially when that person didn't really like him all that much to begin with.

Then the door whisked back, and Sheppard stood in a cool blue pool of light. He was fully clothed and didn't look recently awoken, or murderous. Puzzled and slightly annoyed, yes, but not about to lunge through the doorway and knock Rodney on his ass for waking him up. Peeking around him, McKay could see a book lying open on the bed.

Sheppard raised an eyebrow. This better be good, that look said.

And McKay's carefully planned speech -- involving Harry Daghlian, Louis Slotin, the Manhattan Project and lives sacrificed in the name of science -- flew straight out of his head. Rather than a string of half-truths and carefully selected facts calculated for maximum emotional manipulation, he found himself, unexpectedly, speaking the truth.

"I know you don't trust me, not really." He spoke quickly, before he could lose his nerve. There was a flash of something in Sheppard's eyes -- maybe pain, maybe anger, maybe a little of both. "You and I both know it's true."

Sheppard's arms were folded across his chest like a barricade -- hostile, defensive. "Then why are you here?"

"Because I --" And here he faltered, his supreme self-confidence breaking down. There were words, on the tip of his tongue, that would turn Sheppard to his side. He knew it. He just didn't know what to say, or if he dared say it. And with a growing sense of dismay, he realized that he didn't even know why he'd come here.

It had been easy to imagine manipulating Sheppard when he wasn't standing face to face with him. Now ... now he felt like a man leaning over the edge of a precipice and starting to slide.

If he couldn't make this work, he was going to have to go to Caldwell. Elizabeth couldn't seem to understand -- willfully refused to understand -- the importance of the breakthrough the Ancients had very nearly made on Doranda. It could make the difference in the war effort -- could be the distinction between victory or defeat at the hands of the Wraith. They couldn't walk away now, not knowing, never knowing, letting Collins die for nothing and leaving a puzzle unsolved.

Sheppard was still watching him. He hadn't run him off, and almost for the first time since the whole thing with Ford, McKay wondered if something might still be salvaged of what they'd once had. If only he could make him understand ... and believe. Not by manipulation, but by reaching down and pulling out the well-hidden inner scientist that he'd occasionally glimpsed lurking behind Sheppard's shuttered hazel eyes. Once upon a time, he might have been able to do that. Maybe he still could.

"Can I come in?" he asked hopefully.

Sheppard's answer was quick, flat and immediate. "No."

"Fine." He took a deep breath, trying to compose himself, but instead the desperation spilled out of him in a stream of words that, he feared as he listened to himself babble, made even less sense than usual. "Listen, the Doranda thing ... I can make it work. I know how to do it. I've been over the Ancient's calculations. Three times. I know where they went wrong. I know how to fix it. All I need is to get Elizabeth to --"

"Wait, wait, wait." Sheppard raised a hand. "What are you saying here, McKay? You think you can make this work when the Ancients couldn't?"

"Well, yes, because they were wrong. And I'm not saying that I'm smarter than they were ... necessarily ... but I've got the benefit of hindsight. I know how to make it work, Sheppard. And this is big. This is the wheel, the light bulb, the hot dog big."

He was getting caught up in it, but instead of seeing his own enthusiasm reflected back from Sheppard's face, as he had hoped, all he saw was suspicion. "McKay, one of your men died today."

Oh, that was fine coming from Sheppard; he hadn't even been there, hadn't seen it. Every time he closed his eyes, McKay was haunted by Collins' smoking body, and he suspected it would be a long time before he could sleep without nightmares. This was not something he wanted to get into right now, not with Sheppard. He didn't dare. He was too afraid of breaking down to let himself go there, and so he waved a dismissive hand. "I know, I know, I know, Colonel. But Collins' death is a pointless waste of life unless something comes of this. Don't you get it? There's no better memorial than to make the project work. He'd want this."

The invisible wall between himself and Sheppard seemed to have widened. "Would he, really. Asked his family about that?"

"Damn it, would you forget Collins for a minute? That isn't what matters here! This is so much more." Why couldn't any of them understand? "Even if we can't safely operate Project Arcturus at anywhere near its full capacity, it could still generate the power of a dozen ZPMs. We can power the shield indefinitely. We can make Atlantis fly. We can win the war against the Wraith. Big guns, Colonel, to make hiveships go boom. You know Caldwell's not going to let this go. This'll happen whether Elizabeth gives the okay or not. It's just a question of whether it happens now or later."

Something dark had come into Sheppard's eyes, and he nodded slowly. "You mean whether you get to work on it, or whether they send a team out from Earth once Caldwell gets the all-clear. Is that what it's about?"

"Well -- partly -- and I'd be lying if I didn't see a Nobel Prize in this -- but that's not what I -- Colonel? Hey! Wait!" Sheppard had reached to close the door; McKay jammed a hand in the way, stopping it. "Hey! We're not done here!"

"I think we are."

That was Sheppard's "I'm not kidding here, don't mess with me" tone of voice. There were times when McKay was willing to push back, but he'd already withdrawn his hand before he could think about it, and the door snapped shut in his face.

"It's not about the fucking Nobel!" he shouted at the door. It remained closed. "Son of a ..." He wasn't sure if he meant Sheppard, or himself, or the situation in general.

He wondered if Caldwell was still awake.

------

"I want him off my team."

Elizabeth finished typing a line on the report she was working on, before looking up at Sheppard hovering at the other side of her office.

"Does this have anything to do with Doranda?" After denying Rodney's request for more time to study the Ancient weapon, she'd ordered the address locked out of the database. Caldwell might have that order rescinded on his next trip from Earth, but that was six weeks away and she didn't plan to worry about it until it happened.

He just nodded, tight-lipped, and she saw her own strain echoed in the too-hard lines of his face. Once upon a time, they'd all thought that re-establishing contact with Earth would be the answer to their prayers -- that the cavalry would swoop in to save them, and all the fear and stress and chronic shortages would be a thing of the past. But that was before they'd learned, firsthand, what the residents of the Pegasus Galaxy had been dealing with throughout their history. They'd all lost friends in the siege, lost peers and co-workers who had become like family members. They were at war, and at long last, that cruel reality had finally sunk in. It was a little ironic, to Elizabeth, that they'd all laughed more, enjoyed life more, back in the days when they were on their own and surrounded by enemies on all sides. In a way, having a lifeline to Earth had done nothing more than make them all acutely aware of how isolated they really were.

"He came to my quarters last night."

"Rodney?"

Sheppard nodded. "Wanted to convince me to give the project on Doranda another try. Says he thinks he can fix what the Ancients screwed up."

Elizabeth grinned a little, despite the grim set to Sheppard's jaw. "Well, that's Rodney, John -- he doesn't do things by halves."

"Elizabeth -- he doesn't care. About Collins' death. A man is dead, one of his people, and to him, it's just an interesting scientific puzzle. It's the outcome of an experience, something to mark down on a clipboard before he moves on to the next part of the experiment. He wants to get a Nobel Prize out of this, and he doesn't care who has to die to make that happen."

Elizabeth folded her hands atop her desk, putting the report aside to focus her mind on the problem at hand. She had seen Rodney's face when he'd come back from Doranda -- the raw pain in his eyes. Sheppard hadn't been there to see; he had been training a group of the new Marines, having left scientist-babysitting duties on Doranda to Lorne's team. "John, you know Rodney..."

"Do I? In a way I feel like I never really saw him until last night, Elizabeth. The person that I thought I knew ..." He drew a deep breath and let it out, a bit shakily. "Either the person I used to know never existed, or doesn't exist anymore. The man I spoke to last night -- Elizabeth, I don't want that man covering my back offworld."

Elizabeth nodded once, slowly. "Request denied."

He laughed, a short bark of disbelief. "You think this is a joke?"

"No, John. But I need you to understand that yours is the flagship team of Atlantis. I need the best and brightest out there representing us. I certainly won't go behind Rodney's back and yank him off the team unless you can give me a damn good reason for it."

"Because I think he's a security risk? You don't believe that's a good enough reason?"

"No, John. Maybe that's your latest excuse, but you and I both know that you want him off your team because your friendship's fallen through and now the two of you don't get along. And, I'm sorry, but that is juvenile and silly. You're thirty-eight years old and a military leader, not a fourteen-year-old girl. Whatever personal problems you two have, for God's sake act like adults about it. You can work with someone you don't like. People do it all the time."

The thin line of his lips had grown thinner. "I see."

"Do you? I've given you a lot of autonomy in who you choose to have on your team. I even let you put Ronon on there, against my better judgment. But this is petty, and I refuse to allow you to let your personal problems interfere with your ability to do your job." Seeing the rigidity of his shoulders, she backed off a little -- she had no desire to push him to an explosion. "If you can come back in a few days, a week, a month, and tell me the same thing, and give me good reasons, then I'll talk to Rodney. In the meantime, I'll consider your request; I promise that I will. But this is not something that I want to see done in haste, John."

He just nodded sharply, and turned his back on her, leaving her office with a swift stride. Elizabeth let out a long sigh and tried to focus on her paperwork. She'd just gotten into the biologists' figures on Athosian grain yields when a soft tap on her office door distracted her again.

"Dr. Weir?" It was Caldwell. Just the person she didn't want to see. "We're leaving for Earth shortly. I wanted to know if you've changed your mind regarding Doranda."

She shook her head. "I'm more convinced now than ever that Project Arcturus is a mistake."

He sighed. "I'd hoped it wouldn't come to this. You may not believe me, but I don't want to make an enemy out of you. But, if this can turn the tide in the war against the Wraith, let alone our enemies back in the Milky Way galaxy -- you have to understand why I can't let this go, and neither can the Pentagon."

Elizabeth folded her hands and gave him a polite smile. "Helping the U.S. military acquire bigger and better weapons has never been the purpose of this expedition. I am convinced that the dangers of Project Arcturus outweigh its possible benefits."

"Even if your top scientific advisor says otherwise."

Her heart went cold. This was what she'd been afraid of. "Did he talk to you?"

Caldwell nodded. "This morning. He says he knows why the project failed for the Ancients, and he's confident he can make it work."

Damn it, Rodney. It was what she'd feared. When he couldn't get her on his side, he'd gone to the military -- first John, and now Caldwell. "Unfortunately, confidence is not something Dr. McKay is in any short supply of."

Caldwell raised his eyebrows. "I was under the impression you'd hand-picked the people for this expedition, Dr. Weir. Is this how much faith you have in them?"

She could tell that her smile had become very fixed. "I know my people, Colonel. You do not. I know their strengths ... and their weaknesses. That doesn't mean I don't trust them. It only means that I know the areas where I can trust them less. If you fight me on this one, Colonel, trust that I will fight back."

Caldwell inclined his head with a small smile on his face. "I'd better get back to my ship, Dr. Weir. I'll see you in six weeks. I hope we'll be able to come to an understanding by that time."

Elizabeth watched him leave. She tried to get back to her paperwork, but her brain was having none of it, and eventually she left her laptop open on her desk and walked out to stand against the balcony, watching the gateroom.

It depressed her to see that the delineation between military and civilian had become even more pronounced than the last time she'd specifically looked for it. She remembered a time, not too long ago, when the Marines guarding the gateroom had talked and joked with the computer techs while they all passed the long slow days between crises. Now, though, there may as well have been barricades between them, for all the notice they took of each other. If her chief scientist had begun exploiting those divisions for his own gain, then it was to her, the leader of the city, that the real blame fell.

For a year, they'd all been equals -- pioneers in a brave new galaxy. The castes and cliques of Earth had been left behind along with everything else. But the cracks had begun to show during the Wraith siege, and now that the Daedalus was bringing fresh crew members, the egalitarian citywide family atmosphere had faded away. In a lot of ways, Elizabeth thought, the groups took their cues from their leaders. It had been common, once, to see Sheppard hanging around the labs, but as his relations with McKay grew more strained, those times became rare and tapered off altogether. Rodney had made his dislike of the military clear from the get-go, but it was hard to take him seriously on that subject when he spent most of his free time hanging out in the lounge watching movies with one or more members of the military he claimed to despise. These days, it seemed that he'd decided to act on his beliefs. It had been months since she'd seen Rodney pass a civil word with anyone in the military, including his team, when they weren't on a mission together. And rarely enough even then.

She leaned on the railing, disheartened and just a little bit afraid. If they couldn't make a go of a civilian-run base in the Pegasus Galaxy, she had no doubt that the military would take it over. And the consequences of that frightened her.