Disclaimer: Stargate belongs to Metro-Goldwyn-Mayer Studios Inc, no infringement of any rights is intended. I'm just playing with the characters, roughing them up a bit, but I promise to dust them off and hand them back still reasonably intact when I've finished with them.

Spoilers: Possible spoilers for various episodes from Season 1 through to 'Outcast' in Season 4. The background story for Sheppard contained in this fic is purely my surmising, and not canon in any way shape or form.

Warnings: Scenes of violence and torture and mature themes not suitable for young readers.

Many thanks to Sterenyk Strey for reading this through for me, tweaking my Britishisms into shape, pointing out my typos, and encouraging me to really go for it in places where I was holding back a little. You're a bad influence, woman - but a great beta! ;D All remaining mistakes are mine - they always were and I put my hands up...it's a fair cop!

Summary:

The beginning of atonement is the sense of its necessity. ~ Lord Byron

Sheppard and team find themselves stranded on a planet at the outskirts of the Pegasus Galaxy with a dangerous energy anomaly, a gate that refuses to dial out, and a Medulsan who means to have her pound of flesh. Shep Whump of both the physical and emotional kind – of course!

This is the third story in the Deliverance Trilogy. Stories to be read in this order: Deliverance/Repression/Atonement

The story is complete aside from final edits and will be posted regularly.

Atonement

Chapter 1

It soon became clear that the planet beneath them was much like many of the other 'M' class planets they'd visited when Sheppard took the jumper in low to get a better look – lush forests, expanses of clear oceans, some with pretty impressive breakers, and vast stretches of uninhabited land as far as the eye could see. Nowhere in the Pegasus Galaxy suffered from the population overcrowding Earth did. A little luxury courtesy of the Wraith, he guessed. He'd imagined he would tire of views like this eventually, but he hadn't. Not in all the years he'd been posted out there now. It seemed some things were breathtaking no matter how often you saw them.

If he was honest, Sheppard hadn't wanted to come out so far from Atlantis. Okay, so they were only ever a Stargate jump away, but this little planet lay pretty much on the outskirts of the galaxy, and they had never ventured so far from home before. Things like that wouldn't normally have bothered him, but lately, the thought of something going wrong and leaving them far from help played endlessly on his mind. Still, Rodney had told him the planet purported to house an Ancient research facility, though the partially corrupted data file hadn't said exactly what was being researched there, and where there was a research facility, there was the chance of a ZPM. That was always worth a trip.

He glanced across at Teyla sitting in the co-pilot seat beside him, who gazed with admiration at the beautiful scenery rushing by beneath them, then looked over to give him a brilliant smile he knew was meant as thanks. She hadn't been out with them on a mission now for weeks, and she had practically begged to join them on this one because it was straightforward reconnaissance and so classed as low risk. Although at first he'd refused, her persistence had worn him down. Apparently, there was only so much of Atlantis' splendour she could endure when getting no break from it. So he'd agreed, but with some clear ground rules. She was only allowed to leave the jumper if he could park it within a short distance of whatever it was Rodney was hunting for, and she had to force on a tac-vest and carry a P-90 no matter how tight it was over her growing bump.

She'd agreed to his terms, turning up in an oversized vest that almost slipped from her shoulders, but fitted snugly around her stomach. Her uniform, however, had been out of the question. So, she wore it over some tasteful maternity wear she'd picked up while assisting in trade talks with some of their new neighbours, the soft trousers tucked into her normal military footwear. Since moving the city, they had a whole host of new planets to trade with, and these particular people had been particularly taken with carrots.

Despite the restrictions placed upon her, Teyla looked as if she was thoroughly enjoying the flight, and he guessed that made all his worrying worthwhile.

All the same, he wasn't sorry that their preliminary scans of the planet's surface had revealed very little – and certainly nothing that pleased McKay – because that meant they'd soon be out of there and back to familiar territory. The scientist hissed, tutted and mumbled through various different scans, before thudding back against his seat and declaring, 'Well, yet another beautiful planet on which to settle down and raise a family, but one that is of absolutely no use in furthering our fight against the Wraith.'

'Simmer down, Rodney,' Sheppard drawled 'We're explorers; this is what we do. Sometimes there's nothing to find, that's all.' He instinctively operated the various controls required to change the direction and altitude they were cruising at. 'Besides, we have one final area to sweep, so let's not give up hope just yet.'

'It's just like the last five planets we've checked. The only signs of any development are primitive at best. The most interesting thing about this planet is its axial tilt. The relatively high level of obliquity means they'll experience far more extreme seasons. Hence the number of seemingly abandoned settlements we've seen. The locals probably have to migrate when the conditions change in one area and another becomes more favourable.'

'Fascinating,' Sheppard mumbled, stifling a yawn.

'So the people who live here are nomadic?' Teyla asked, her interest seemingly piqued.

'Only in the broadest sense of the word. I expect they spend months in one place before needing to move again. I can't say how long for sure without proper monitoring, but one thing I can tell you with absolute certainty is these people can't help us, so we might as well head back to the 'gate – hello!'

'What is it, Rodney?' Teyla asked, all of them reacting to the telltale tone of his exclamation.

'I'm not sure. I saw something...and then it was gone.'

'What do you mean "gone"?' Sheppard asked, peering back over his shoulder at him.

Rodney scrolled through the last data collected. 'It was an incredible power spike, accompanied by a lower-level surge located just a few miles from here...but it was gone in an instant.'

'Where was the bigger spike?' Sheppard asked.

'Approximately twenty miles north east of our position.'

'Are we talking ZPM big?'

'Yes...maybe bigger for a moment.'

'Might be worth checking out,' Sheppard suggested, although feeling a little pissed that they wouldn't be heading back home after all.

'Yes...yes it might...Oh, wait a minute. Now that's just not possible...'

Sheppard's stomach sank. In his experience, when Rodney started saying things like, "That's not possible" or "That can't be right", things pretty quickly went south.

'What is it?' he demanded, his words carrying a far more urgent stress than Teyla's earlier version of the question.

'I just picked up exactly the same type of spike only five miles to our west,' Rodney reported.

'So what's causing it?'

He could almost hear Rodney's eye-roll along with his petulant sigh. 'I don't know. I would have thought the "that's not possible" line was a give-away.'

'How can it jump around like that?' Ronon added, even his normal calm baritone carrying a slight nervous edge.

'Again I say I don't know...yet. Gimme a few minutes.'

A blinding flash caught Sheppard's attention, to their left and not far away. It hung in the air at what he estimated was the same altitude they were maintaining, causing him to shield his eyes while steering the jumper away from it.

'What the hell was that?' he yelled.

'Same thing!' Rodney called to him, his voice now cracking with panic. 'That one was only a little over one click away.'

'Well, that thing looks like it's making a b-line for us, so I say we abort this mission, head back to the gate and get the hell outta here before it comes any closer,' Sheppard barked. 'Teyla, get ready to dial Atlantis when we're in range.'

Teyla reached out to begin programming Atlantis' address into the DHD, but was almost thrown from her seat by a jolt that shook the jumper and sent it careening to the left.

'What just happened?' Rodney shrieked, gripping his seat.

Sheppard called up a diagnostic, hardly able to believe what it told him. 'We've lost our right engine pod.'

'Okay. Lemme see if I can fix it,' McKay instantly responded, trying to lever himself up and out of his chair.

'Stay put, McKay. There's nothing to fix. When I said we lost an engine pod, I meant it!'

He shot a look back, seeing the utter disbelief register on the astrophysicist's face. 'Oh, crap!'

'Okay, people, hang on to your seats – we're going in,' Sheppard yelled, steering for something... anything...that might cushion the fall.

From the corner of his eye he saw Teyla brace herself against the control panel, and he told himself he had to get this right. She was carrying an unborn child; if he didn't, she could lose it. Dammit! Why had he agreed to let her come? She'd stayed safely on Atlantis for weeks now, why had she picked today of all days to ask to join them?

Forcing himself to focus on their current dilemma, Sheppard headed for a patch of woodland, which he calculated they could just about make at their current velocity and rate of decent. Hopefully, skimming the trees first would lessen the impact with the ground.

'Okay, here we go,' he warned as the branches loomed up in front of them. A brief whimper from Rodney was the last thing he heard before the jerk of the collision threw him forward into the flight controls and everything went black.

*****

'John...John...can you hear me?'

Teyla's voice fought its way through the haze and aching to bring him reluctantly back to his senses. Sheppard strained open his eyes to see her pretty and reasonably unscathed face smiling back at him.

'He is awake,' she said, turning to someone behind her.

'About time,' McKay grunted. 'At least now we can get out of here before the whole thing falls to the ground.'

That helped to rouse him. Sheppard snapped his head up, only then realising the aching wasn't confined to his head alone, but to his neck vertebrae, too. 'Wha' d'ya mean?' he slurred, suddenly realising he could only see branches out of the windshield.'

'We seem to be caught up in the branches of one of the larger trees in this stretch of woodland,' Teyla explained. 'But our position is precarious, and has already shifted twice. We should get out as soon as possible.'

'Sounds like a plan,' Sheppard agreed, ignoring the sensation of sticky heat trickling down the side of his face. 'Ladies first.'

Teyla didn't argue, a sure sign that she fully understood the danger of their situation. As she edged to the back of the jumper and lowered the hatch, Sheppard and Ronon did their best to maintain the balance for her. 'You sure you can manage that okay?' Sheppard called to her, feeling off kilter himself now, even if the ship was holding steady.

'I have climbed many trees in my time, Colonel. This will be no different,' she assured him, slipping her kit onto her back.

'Except you weren't five months pregnant last time,' Rodney pointed out, shrinking under the pressure of three withering glares.

Teyla, disappeared out of the back of the craft, radioing up to them once she was clear of the possible landing site should it fall. Rodney was next, though he was quite vocally against the whole process. Apparently, not only were enclosed spaces not Rodney's thing, but neither were heights – nor trees, for that matter.

Sheppard knew it would be next to impossible to persuade Ronon to leave before him, and he was right, so took advantage of the Satedan's extra weight to throw some emergency kit out of the back of the craft before taking his own pack and climbing out slowly while Ronon adjusted his position to maintain the equilibrium.

Once he was down, Sheppard wasn't in the least bit surprised to hear a primal scream as Ronon launched himself from the craft and threw himself into the waiting branches of a neighbouring tree. Seconds later, the jumper took a nosedive, crumpling on contact with the ground. Although he'd known the craft was next to useless now, it still stung to see it take that final plunge.

With agility defying his size, Ronon swiftly joined them on the ground, a boyish grin almost splitting his face in two. 'Well, there you go, McKay. You got your wish. You found somethin'.'

'This wasn't quite what I meant,' he moaned, looking decidedly haunted.

'That'll teach you to be careful what you wish for,' Sheppard quipped, wincing as a pain like a hot poker stabbed into his brain just behind what he could now feel was a small but reasonably deep gash above his right eyebrow. Just what he needed. They had to be at least eight clicks from the gate, and now he was going to have to make that trip with a crushing headache at best, if not a brewing concussion.

'Everyone okay?' he asked, now they had the time to examine themselves. 'Teyla?'

'I am well enough,' she assured him, tying back some strands of hair that had worked loose from her partial up-do.

'And the baby?'

'The baby is fine,' she smile, dropping her hands to her stomach now her hair was secured. 'Although the excitement certainly seems to have woken him.'

'That's good. Everyone else?'

'I think I bruised my knee...' Rodney muttered, trying to roll up his trouser leg to check.

Sheppard ignored him, looking at Ronon, who, though covered in minor scratches from his skirmish with the tree, seemed otherwise unharmed.

'What about you?' the Satedan asked. 'That looks painful.'

'I'll be fine,' Sheppard told him, but even as he said it, another pain bolted through his skull making him suck in a sharp breath.

'I think we should attend to your injury. I have Steri-strips in my medical pack,' Teyla told him firmly, laying her hand on his shoulder and making him sit down.

So he let her do her thing, mothering him and cleaning up his cut until it was ready to pull back together with a few sterile strips. Then, she handed him a couple of Tylenol and would not take refusal as an answer.

'We have plenty more. There is no point in you struggling on pain if we can make you more comfortable.'

'I guess not,' he agreed, rubbing his sore neck. 'Okay, let's head back to the 'gate and get the hell outta here.'

Somewhere in the distance they heard a crack, and a flash lightened the sky for a few seconds before fading again.

It didn't take a genius to work out that was the same anomaly that had buzzed them and wiped out the engine pod, and from a quick glance round at the faces of his team he knew they realised that, too.

Without another word, they set off in the direction of the 'gate at a healthy pace.

*****

After almost an hour of walking, and with his headache still nagging despite the medication, Sheppard stumbled and fell, prompting a collective cry of concern from his colleagues.

'I'm good,' he insisted, grasping Ronon's forearm and allowing his friend to haul him back to his feet. 'I tripped, that's all.'

'Maybe we should rest,' Teyla suggested, her cheeks flushed and her forehead damp with perspiration. 'I am feeling rather tired myself.'

'Oh, well, if you and junior need a break...' He knew she was only giving him the excuse he needed to take a time out, but he accepted the offered opportunity with good grace regardless.

The air was heavy with moisture, the clouds now gathering overhead grey and foreboding. It was only a matter of time before rain set in, and they still had two miles to walk at least. He dabbed at his brow, finding only a slight hint of blood on his fingertips as he drew them back. At least it was congealing now, even if he was building up to the mother of all headaches again.

'I'm picking up some signs of development not too far from here,' Rodney reported from his perch on a nearby rock, knees bent up almost under his chin with his tablet resting on top of them. 'Just about where that smaller power spike occurred.'

'I thought we'd decided we were heading back,' Sheppard called over to him, hoping he would drop the subject.

'Well, these structures are pretty much on route – only a half a mile out of our way. They might be worth a quick look.'

Though all he wanted to do was get back to Atlantis, take a hot shower and get some rest, Sheppard figured Rodney might be right. At least if they found something useful there the mission wouldn't have been a total bust.

So, once his legs felt like they could take the strain again, they followed McKay toward the buildings he'd picked up on his scan.

The extra legwork seemed all the more promising when the structures turned out to be of obvious Ancient design. The place was half-ruined and overgrown by some kind of ivy type plant and creeping weeds, but there were still some pretty interesting looking devices in there, all lying dormant.

Sheppard strolled around them, keeping his gun in his hands as he let his eyes roam over the various panels and screens. Since losing the jumper, he'd had an almost irrepressible desire to get back to Atlantis and safety, but he also knew that wasn't entirely down to the powerful anomaly that had disintegrated their engine pod. He'd been feeling this way for weeks now, and there was only one person to blame...

'Colonel, can I speak with you in my office, please?'

The request seemed simple enough, depersonalised somehow by the slightly tinny sound of the voice filtering through his earpiece, but something in Sam's tone told Sheppard this wasn't going to be one of those average everyday chats. He agreed and made his way there, finding Sam sitting unnaturally upright behind her desk and looking grave. If he hadn't known better, he'd have assumed she was being held at gunpoint.

'Sit down, John,' she said, watching him enter the room and take up a chair in front of her.

She flashed him a smile, but it was tight and over very quickly and lacked the natural warmth it normally exuded. Her legs were crossed and he couldn't help but notice the way she tapped her foot, rapid and erratic; something was obviously troubling her.

'So, what's this about?' he asked, keen to move things along. He was on a tight schedule today; he and his team were heading out to M6R 377 to check out an Ancient structure spotted by a MALP when they sent it through and he'd been on the way to the armoury when Carter had contacted him.

'We've received a communication from Medulsa –'

For a moment, Sheppard's brain simply phased out. He knew the news was going to be bad because Sam wore the sort of expression that said she felt sorry for him and her hands lay clasped on the desk, knuckles white with tension. This was bad, definitely bad. He ordered his grey-matter to pull itself together and focus on her words, just as she was finishing up something that sounded every bit as terrible as he'd feared.

'...so, with the head start, there was no hope of stopping her before she got to the 'gate. I'm sending a team down to gather the last fifty gate addresses dialled, but –'

'—but she could be anywhere by now,' he finished for her.

Sam nodded. 'Pretty much.'

'Was anyone hurt?'

She didn't even have to say yes – the pained way her mouth twisted at the question, and the deep swallow told him someone had. He sank into his seat, letting his head fall back as he stared up at the ceiling even before she told him who.

'She knocked a young man senseless when he opened her cell door to leave her some food and water. We don't know yet whether there will be any lasting damage. Dr Keller has him in the infirmary under observation; we'll know more once he regains consciousness.'

He nodded, his lips pressed hard together to hold back any kind of inappropriately emotional response. 'I have to get going now, but I'll get an update on his condition as soon as I get back.'

'Actually, I was thinking maybe you should sit this mission out. Major Lorne is ready and willing to head up the team today, and I really would like to discuss this problem further with you. You're pretty much our resident expert on Sarayah since Kate died. She's refused to speak with Dr Weissman at all since he got here. She apparently has a problem with the fact he's a man.'

He didn't want to agree to her request, but had the distinct impression she was holding something back. Why did everyone do that to him where Sarayah was concerned? Stupid question; they held back because he was still holding back. 'Okay...as long as you tell me the whole story this time.'

She flashed that same strained smile, tapping her earpiece and giving Lorne the go-ahead to take up Sheppard's role on the mission.

'Sheppard...Sheppard! Where is your head at? I said I need you over here.'

Rodney's acerbic demand pulled the colonel back from the uncomfortable memory that had played over in his mind more times that he cared to recall now. He dragged his eyes away from the window he'd stopped in front of while staring sightlessly out across the landscape.

'What is it, McKay?'

'I said I want you to come over here and try to activate these things. They've been powered down for a long time. Perhaps they just need someone to initialise them.'

'Well, you have the gene...'

'Yes, and I've tried already. But you have a natural representation...on occasions the synthetic gene isn't enough.'

'You know, sometimes I get the feeling you only want me for my body,' he smirked, waving a hand over numerous serious looking devices that mockingly remained inert.

'Oh, ha ha. So that's me and most of the female population of the Pegasus Galaxy...oh...present company excepted, of course.'

Teyla just rolled her eyes, strolling away and shaking her head.

Sheppard chose to cover his embarrassment with more bravado. 'That's not my fault, Rodney. I guess I just have a natural and irresistible charm.'

'Is that right?' Rodney tried a few more things, then dropped his hands to his sides with an exasperated sigh. 'Well, I hope you don't find you haven't lost your touch with women recently, because you've certainly lost it with Ancient tech. These systems are useless. I'm getting minimal power readings – nothing strong enough to power them up.'

'And that's not my fault either,' Sheppard snapped, losing his cool with Rodney's choice of material now. 'This stuff's obviously out of juice. What would you like me to do, pull a ZPM out of my ass?'

'That would be helpful if you could manage it, yes,' Rodney fired back. 'Failing that, a naquadah generator might do.'

Sheppard simply glared back at him. This was an argument that had been on the cards for weeks, and he had no idea why Rodney was insistent on pursuing it. 'What's your problem, McKay? It's not my fault the jumper crashed, or that this stuff doesn't work, so why are you biting my head off?'

'Well, maybe I'm just tired of all the pussy footing around we have to do with you lately. Maybe I just wish you'd admit you're stressed and that's why you're cranky with me.'

'I'm not stressed, and I'm not cranky. That's your job,' Sheppard grunted, fixing Rodney with his best "drop it now" stare.

'You've been like this for the past three months since that woman got free –'

'Rodney!' Teyla hissed in warning, throwing him a death glare.

Rodney just folded his arms over his chest and stood firm. 'Oh, that's right, I forgot. We're not supposed to talk about her in front of Sheppard, are we?'

Teyla and Ronon exchanged an awkward look, as if they knew the trouble that comment would cause.

Sheppard looked around at them all, feeling hurt. 'You've been talking about this...behind my back?'

'Only because we were concerned about you. Rodney is right, you have seemed a little distracted since the news of Sarayah's escape,' Teyla tried to reason with him.

Sheppard shifted his gaze from her to Ronon, then to Rodney, neither of the latter two able to maintain eye contact beyond the briefest of moments. 'I didn't realise this was such a problem for you guys,' he spat, annoying even himself with the venom in his words

'That is not what we meant, John,' Teyla said, reaching out to rest her hand on his forearm.

He shifted just enough to break the contact. 'Really? So what do you mean?' he demanded, tilting his head and narrowing his eyes at her. So now he was picking on Teyla, taking his insecurities out on her. Nice one, John. Way to alienate your friends.

'We approached Dr Weissman for advice on what to do once we learned of what Sarayah had done while escaping. He told us we shouldn't speak to you about it...that you would talk to us when you were ready –'

'A theory I completely disagreed with, I'd like to add. Things like this are better out in the open...clear the air and all that,' Rodney rambled, his smug smile fading as Sheppard turned his icy gaze on him.

'And that's why you're an astrophysicist and not a psychologist,' the colonel sneered, again angering himself with his churlishness. The thing that pained him most was that they were right; he had been distracted since the news from Medulsa, and he'd known the nightmares and the paranoia were getting out of hand, but he'd been too stubborn to seek help, convincing himself he had it all in hand.

'We can't do anything here. I say we head back to the 'gate and report what we've found to Carter,' Ronon suggested, playing the role of peacemaker for once.

If Ronon felt the need to diffuse the banter between him and McKay, Sheppard knew things had sunk to an all time low. The Satedan pretty much lived for it.

'I second that,' he breathed, pushing past McKay and heading for the fractured doorway back to the outside world.

They covered the remainder of the ground between the ruined Ancient outpost and the Stargate in almost complete silence, other than the occasional gripe from McKay about ill-fitting boots. For once, everyone let it slide.

Rain set in, soaking them through to their skins and adding to the air of gloom, an atmosphere Sheppard knew he'd created and now felt bad about. But no matter how much he told himself his team's interference was coming from a good place, a place of concern, he resented the fact they had lost faith in him to some degree. He had their backs, he always would have; he wasn't so distracted he couldn't still protect them. And he felt like he needed to protect them, now more than ever. It was his fault Sarayah was out there somewhere, probably plotting some way of getting back at him, because he could have killed her out there in the desert plains of Karafus, and he hadn't. That had been a mistake, a big one, and one he now bitterly regretted. Sometimes, compassion was his worst enemy. It either made him pull back from doing the things that needed to be done, or hounded him relentlessly if he saw them through.

At the 'gate, Rodney began to dial without waiting for Sheppard's instruction, and the colonel scoured the surrounding land, ascertaining there was no nearby threat. All was clear, and he heard Rodney angrily slam his hand down on the centre of the DHD to activate the wormhole home.

A flash in the distance caught the colonel's eye, but then a whine reminiscent of a dying dog caused him to snap his head round, the lack of an event horizon setting his heart running a little faster. 'McKay?'

'Must've mis-dialled,' he murmured, but the way his forehead had puckered suggested Rodney knew he hadn't and was worried.

Sheppard watched him this time as he methodically and firmly struck each symbol, then finally pressed in the centre point, sending the address to the 'gate. Another baleful complaint grumbled out from the 'gate's failing connections.

In the distance, the light still flickered as if waiting to see what would happen. Its presence only emphasised the failure of the wormhole, increasing the urgency of their desire to make it work.

Without a word, McKay tried it again, slapping down hard on each key with increasingly jerky movements, as if he thought additional speed and force might be the key to the problem. The repeat of the disheartening groan clarified that wasn't the case at all. Thankfully, the anomaly faded without causing them any further problems.

Sheppard stared at Rodney and silently willed him to come up with something obvious, something he could do to fix things. The scientist prised off the panel covering the control crystals, muttering to himself as he worked, attaching his tablet to the device to run a diagnostic. The noises he made as he did so were no more promising than those that had issued from the 'gate itself.

Eventually, Rodney looked up, eyes huge and face pale. 'Er...this may be a problem.'

And somehow, that just didn't surprise Sheppard at all.