Title: Broken

Rating: PG +13 (violent scenes later in the story)

Disclaimer: Stargate belongs to Metro-Goldwyn-Mayer Studios Inc. No infringement of any rights is intended.

Spoilers: Quotes from the transcripts for 'Real World' and 'Lifeline', and spoilers for numerous episodes up to and including 'Lifeline'.

Summary: AU following the events of Lifeline. Elizabeth is discovered abandoned on a desolate planet after her abduction by the Asurans. Sheppard and his team struggle to come to terms with the fact they left her behind and the feelings of mistrust of their former leader now evokes in them. Did the Asurans really abandon her because she was able to withstand their attempts at questioning, or is her return to Atlantis the trap they all suspect it is? The strain begins to take its toll on them as they struggle to cope with a damaged city and the dangerous situation Elizabeth's presence amongst them creates. As friendships fall apart, can they rebuild the bonds they once had, or are they forever broken?

Character death, but one presented in canon.

This story is complete apart from final editing and will be posted at regular intervals.

Chapter 1

The Asurans stood frozen all around them as Sheppard and Ronon made their way back to the jumper. It was as if they'd walked into the middle of some kind of crazy 'Living Statue' mime convention, except the colonel was pretty sure these guys would do a lot more than push against an imaginary stiff wind if they got moving again. Sheppard knew this had to be down to Elizabeth and was glad Rodney's kill switch had malfunctioned. All they had to do now was find her so they could all get out of there. He activated his earpiece to contact the scientist.

'Still nothing from Elizabeth?' he asked.

'No. Can't communicate with her; I can't track her; it's like she just – she just disappeared.'

'Well, if she's the one who froze the Replicators, that means she's probably still alive,' Sheppard replied, finding some comfort in that thought.

'For the moment, maybe,' he heard McKay reply.

'She can't be that far,' Sheppard reiterated, refusing to listen to him.

'We'll find her,' Ronon rumbled, adding his support.

'Well, you'd better make it fast. These Replicators could unfreeze at any time,' Rodney told them.

Aggravated that McKay always felt the need to state the obvious, Sheppard barked back, 'Thanks, Rodney!'

They ran around the next corner and stumbled right into the final stages of Elizabeth's mental battle with Oberoth. The huge Asuran was on his knees and had hold of her arm, her hand positioned as if she had penetrated his skull the way the Replicators had done to them in the past, but he had now pushed it back from him.

'Elizabeth!' Sheppard forced the word out, even as his throat began to constrict in panic. He could see the situation unfolding in front of him, but there wasn't a damn thing he could do to help. They were going to lose her to the Replicators, an enemy even more formidable than the Wraith.

'Get to the jumper,' she shouted back to him, her sheer willpower the only thing standing between them and Oberoth's frozen minions. She looked so fragile compared to the huge, bulbous Asuran that it tore his heart out to admit she was right and he would have to leave her there in this facsimile of Atlantis. The place was as hostile and repugnant to him as Atlantis was welcoming, and he couldn't bring himself to back away.

'You're coming with us,' he insisted, refusing to leave. Behind him, Ronon sent an ARG shot Oberoth's way, hitting him, but having no real effect. They had adapted already. They were defenceless.

'I can't keep them frozen much longer!' she yelled, her voice cracking with panic.

'We're not leaving you behind!' he shouted to her, postponing the inevitable for just a few moments longer. Something...he had to think of something.

'If you don't leave right now, none of us will get out of here, so go.' She turned her head slightly toward him. 'THAT'S AN ORDER!'

He felt compelled to rush in and drag her away whether she'd given him an order to leave or not. But the ZPM waiting for them on the jumper meant he couldn't risk it. The city and everyone in it would die without it. He had to sacrifice the life of one to save many...even if that one life was Elizabeth Weir.

Oberoth let go of Elizabeth's arm as the Asurans began to fire on both Sheppard and Ronon, forcing them to duck. But still the colonel could not leave. He felt Ronon catch hold of his Tac Vest and drag him away. 'Come on!'

For a moment or two he struggled against the huge Satedan, but with a sense of inevitability he gave in and followed him. He called out to her again. 'Elizabeth!'

'Go!'

The fear in her voice tore into him. She turned and his eyes locked with hers as the Asurans rushed forward and caught hold of her arms, restraining her. He held her gaze until Ronon dragged him out of sight...

With Elizabeth's order still echoing in his head Sheppard woke, gasping in each panicked breath. Had he shouted her name out loud? Probably, but hopefully no one had heard him. His face was tacky and sweat soaked through his T-shirt where his back pressed against the mattress. He felt more like he'd run 10k than slept for half an hour. Half an hour. Was that really all he had managed? He sat up, swinging his legs out from under the covers to allow the air to cool them. He didn't feel ready to go back to sleep just yet.

The dream he'd woken from was the same one he'd relived time and again for the past three nights since they'd carried out the raid on Asuras, and he held out no hope it would stop recurring any time soon. Having cooled off in his air-conditioned room, his shirt now sat cold and uncomfortable against his skin, so he slipped it off and shuffled to his bathroom to freshen up, splashing cold water on his face, chest and back to relieve the burning sensation in his fevered body. He leaned on the sink and stared into the water, reliving the events of his dream one more time in his mind's eye. He'd refused to follow orders he disagreed with less than that one. Why had he left Elizabeth to the Asurans? If he hadn't hesitated – if he'd just acted instead of thinking about it – he might have saved her and held onto the ZPM, too. Of course, breaking her hold to remove her from the Replicator city would have released Oberoth and the hundreds if not thousands of Asurans she'd immobilised too soon for them to get a head start. But there had to be a way he could have saved her. He just hadn't been smart enough to think of it when he needed to – still couldn't work it out now, in fact.

He looked at himself in the mirror hanging above his sink, staring into his sunken, bloodshot eyes and fighting with the urge to smash his reflection. He didn't want to look at himself anymore; he'd let down one of his best friends, and he couldn't imagine how he could face that truth day after day. But smashing the mirror wouldn't bring back Elizabeth, and neither would it appease one iota of the sense that he'd betrayed her. He would simply have to find a way to cope somehow.

The worst thing was knowing he had flown her straight into enemy hands. He and his team had talked her into a heist that was always going to put her at high personal risk, and now, not only was Elizabeth in the clutches of the Replicators, but also all the knowledge of Atlantis she held, which, quite frankly, was a frightening amount. There was no way Elizabeth would be able to resist their mind probing forever, even with the enhancements of her operative nanites. Actually, all it would take would be a little reprogramming and those damned nanites would probably make her tell them everything she'd ever learned about the city and the Ancients, and about the effectiveness of their defences. Their best hope was that Oberoth had been so enraged by her actions that he'd killed her outright, and even that didn't bear thinking about. Nausea churned in his stomach, and, deciding he didn't even want to try to sleep anymore, he pulled on his trousers, boots, and a clean T-shirt and headed for the Mess hall.

The corridors were silent except for the background hum of Atlantis itself. Most personnel were tucked up in their beds asleep – all except the skeleton crew required to keep an eye on things overnight, and the scientists taking shifts to repair everything damaged in the Asuran attack and other systems that seemed to be simply giving up the ghost after the strain of their escape. He kind of liked the city when it was quiet like this. At night, he felt his connection to the place so much more clearly; it almost vibrated through every cell of his body, telling him he was meant to be there, that all the events of his life – both good and bad – had been designed to culminate in his decision to travel to this lost city. His life on Atlantis had felt complete, but with each loss, a little bit of that fulfilment ebbed away from him, and now, even alone and enjoying the way the city sang to him, it just didn't feel the same any more. He really needed to get to the Mess hall and drown his sorrows in coffee.

All the way there he kept focussing on how good it would feel to grab a drink and sit out on the balcony area in the cool night air, just relaxing and trying to empty his mind of the problems their bustling daytime hours threw at him. He still felt uncomfortably sticky and knew getting some fresh air was exactly what he needed to feel refreshed...physically if not mentally.

Unfortunately, his plans for caffeine and solitude were dashed the moment he walked into the Mess hall. Rodney was already there, sitting at one of the tables nearest the counter, head buried in his laptop as usual. The subdued evening lighting meant he was partially hidden in shadows, but his laptops screen illuminated the tiredness etched into his features, painting his face with a sickly pallor.

For a second or two, Sheppard considered heading straight back out and foregoing the drink, but he wasn't quick enough. McKay spotted him before he could perform his strategic retreat.

'Sheppard. Couldn't sleep either, huh?'

The scientist looked pleased to see him, and he didn't have the heart to walk away. With a sigh, he headed to the percolating coffee pot, helping himself to a mugful. Rodney had clearly made enough to keep himself going for a few hours; Sheppard supposed even he wouldn't mind sharing one cup with a sleepless friend.

He trudged heavy-legged to the table where Rodney was working and slid into the seat opposite him, slouching as he watched his friend work. 'What's keeping you up?'

'Oh, I'm just doing some more power calculations to work out what additional defensive and offensive tech we can bring on-line thanks to the new ZedPM...once we've carried out all essential repairs that is. I swear something else trips out every hour.'

Sheppard nodded. 'Yeah, that might be wise.'

'D'you think they'll come after us?' Rodney asked, his face as devoid of irritation as Sheppard had ever seen it. Perhaps even McKay got too tired to rant sometimes.

'I'd say that's a given,' Sheppard admitted. 'But we do have one thing in our favour. They don't know for definite where we jumped to once we got the hyperdrive working. And Pegasus is a big galaxy...'

'That's two things,' Rodney pointed out.

Sheppard let that slide; he had neither the energy nor the inclination for their normal banter. He was just glad Rodney didn't seem to share his worry that Elizabeth might tell the Asurans where they were headed if probed by Oberoth, although that could just be the dulling effect of utter, mind sapping fatigue. Right now, with Atlantis in no condition to make another trip through hyperspace, all they could do was sit tight and hope the replicators didn't turn up to finish the job they'd started. No point in telling people they were sitting ducks.

'Anyway we know the attack code was activated. They're going to be busy with the Wraith for a while,' the scientist said with just a hint of smugness that irritated Sheppard more than usual.

Sucking in his cheeks, Sheppard held back the urge to list Rodney's previous failures, but knew it was time to bring Rodney down to Earth...or rather M35-117 where they currently resided. 'And you think they can't do anything else while they're doing that? We already know how tampering with their base code backfired once before. Those nanites are way beyond our current understanding and I think it's about time we acknowledged that. We need to concentrate on other ways of dealing with them...once the Wraith are defeated, of course.'

McKay looked embarrassed, his eyes darting about and seemingly unable to settle on any one thing. 'I know I've said this before, Sheppard, but I'll say it again. I'm sorry for turning the nanites back on.'

Sheppard lifted his tired, dry eyes to his friend's, seeing the sincerity in Rodney's sad face, even if he couldn't meet his eye. He hadn't meant that when he'd made the comment, at least not consciously. But, if he was completely honest with himself, he was still furious with Rodney for reactivating the damned things. They'd discussed it, and he'd told him not to do it unless he was absolutely certain they could repair Elizabeth's injuries and then be turned off again so they posed no further threat. But Elizabeth's condition had rapidly deteriorated, he hadn't been around to act as the voice of reason, and Rodney had panicked. It was understandable, but his mistake had both helped and hindered in so many ways it left the colonel uncertain how he should really feel. Right now, he was battling the almost irresistible urge to smack Rodney upside the head for not following his orders, yet, at the same time, he knew he'd broken so many orders and rules himself in the past few years it would be nothing short of hypocritical. But they'd lost Elizabeth, one of the best friends he'd ever had, and somewhere inside he felt a gulf had opened up he could never hope to fill.

'It's okay, Rodney,' he ground out, knowing that was what McKay needed to hear. 'You couldn't have known how this would all end...and we did get the ZPM we needed. Your actions ultimately saved a lot of lives.'

'And so did your decision to leave Elizabeth behind. So, when are you gonna stop beating yourself up over that?'

Rodney was a far more insightful man these days than he had been at the beginning of their expedition, though his diplomacy still left something to be desired. Sheppard had chosen to work with him because he was commanding Atlantis' primary team and he wanted the best people with him. But there had been several times in those early days when he'd questioned that decision. He'd rarely worked with none military personnel prior to this posting, and McKay's constant whining and pessimism had taken some getting used to. The loss of Ford had been the man's first mellowing point, and Carson's death a few weeks ago had hit him hard since the two had become firm friends in their three years together – despite their constant badgering of one another. Elizabeth's loss would be another stepping-stone in his development – a humbling one once the dust had had time to settle, he hoped.

'I keep asking to mount a mission to go back and extract her, but the IOA are stonewalling any requests I put through. I can't believe they're unwilling to see what a risk leaving her in enemy hands is,' Sheppard sighed, swirling his drink in the mug he clutched.

'Perhaps they weighed up the odds and thought the threat we face now wasn't as bad as the potential danger of several of us ending up in enemy hands,' Rodney pointed out, his voice a little squeaky as if he was afraid of how Sheppard would react to his statement. 'Not wishing to toot my own horn here, but if they caught me, this place would be in serious trouble.'

Though he knew McKay was right, his lack of modesty didn't help the way Sheppard was feeling right now. 'Whose side are you on, McKay?' he demanded, staring his friend down.

No doubt still remembering how close he'd come to a take-down when he'd refused to shut off Elizabeth's nanites, Rodney dropped his gaze to his laptop in an effort to appear less confrontational. 'Yours, of course,' he insisted. 'And you know I'll be right there the minute they give you a green light to go after her.'

Sheppard huffed, looking out of the window. 'Yeah, well, I don't think that's gonna happen any time soon,' he grumbled, taking a swig of coffee. He grimaced as it hit the back of his tongue. He was a fan of strong coffee, but Rodney's recipe was enough curl the hair on his chest. 'I think our best chance is to wait until they choose a new commander for Atlantis, then I'll appeal to whoever that is directly. Maybe they'll bend a few rules for me.'

'Any idea when that will be?' McKay asked.

Sheppard shrugged. He suspected Rodney was harbouring hopes the IOA might choose him, but he doubted they would. Rodney's reputation for tantrums and his overwhelmingly underdeveloped people skills pretty much ruled him out. 'The IOA are so bound up with red tape I doubt even they know yet. That said, I don't think they're gonna want to leave me in charge for too long. I'm not exactly their blue-eyed boy.'

'Yeah, well, they don't know you the way we do,' Rodney muttered. Shockingly, the colonel realised that was pretty damned close to a compliment, and he had no idea how to respond. He ignored it; it seemed the easiest thing to do for both of their sakes.

'Well, it's business as usual until they send through the newbie,' Sheppard said by way of a change in topic, yawning and stretching his tired limbs before clasping his hands behind his head. 'Tomorrow, we head out on yet another reconnaissance mission to seek out more allies and ZPMs.'

'Well, one of these days we have to get lucky, right?' Rodney said, giving him a lop-sided smile that faded far too quickly.

'We're lucky to survive each day, Rodney. An extra ZPM would be like all our Christmases coming at once.'

'That's true. Could you imagine the ways in which we could boost our defences if we had all that extra power in the system?' Rodney beamed, his face literally lighting up at the thought.

Sheppard could see he'd ignited the scientist's enthusiasm and decided this might be a good time to bow out of the conversation. 'Well, my bed is calling to me, so I guess I should head back to my room and try to get some rest.'

'Yeah, okay. I might just do some work on the best systems to boost if we ever do lay our hands on that elusive second ZedPM. I'll see you in the morning.'

'Don't stay up all night, Rodney. Remember we're out on reconnaissance tomorrow.'

'Another hour tops, I swear,' Rodney said dismissively, and Sheppard knew that was a lie, but let it go. Rodney was probably having as many nightmares about what he'd done as he was, so he couldn't blame him for trying to distract himself with work.

He meandered his way out of the Mess hall, and took a transporter to another part of Atlantis, one where he was unlikely to be disturbed. Then, he found that nice, quiet spot he'd been hoping to find out on one the city's east pier and sat down to enjoy the stars and the cool breeze that ruffled his hair and brought his follicles to rigid attention. He didn't mind being cold for a while; it beat waking up in a fevered sweat every few hours. Sitting down to dangle his feet over the edge, he ran over the scenario on Asuras yet again, certain he'd missed something vital he could and should have done to help.

So many things had gone wrong with that mission it was a miracle any of them had escaped Oberoth's clutches. He supposed he should be grateful he'd managed to get Ronon and Rodney out of there so they could live to fight another day. But until he got clearance to go and look for Elizabeth, he felt like he was caught in Limbo, neither completely entrenched in the world that existed prior to losing her, nor comfortable about the thought moving on without her. Atlantis had been Elizabeth's vision; she'd been the one to push it through, and the one who had fought so hard to stay and lead it. Now she was gone, and he didn't know what to do. He knew it wasn't really his fault the enemy had taken her, but at the same time he felt it was. This had all happened at a time when he was in charge of Atlantis; the responsibility for any mishaps fell squarely on his shoulders as far as he was concerned.

He lay back on the metal pier, feeling the ridged, solid metal press into the skin of his back through his thin black T-shirt. It was cold and uncomfortable, yet despite that, he soon felt himself succumbing to the pull of restless slumbers...