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Fanfiction: The Atlantis Trilogy - Part III

For disclaimer and author's note see Part I.

Part 3: Rise and Fall

John couldn't help the nerves that rattled through him as he stepped into the second elevator. The Airman escorting him looked perfectly serene despite the crush of people that got on and off as they made their way down to the lower levels.

It was John's first time in the Cheyenne complex. Mostly he couldn't believe he'd spent the last three weeks in limbo while the Pentagon determined whether to keep him on Earth or send him with the expedition. He'd kind of thought that having agreed to go, he'd go. He'd received confirmation of his transfer to the Stargate programme and arrived back in the States for training only to be told by the General that there was a debate about John's exact deployment because of his mutant gene and he was on leave until further notice. John might have known military bureaucracy wouldn't make his transfer that easy.

He'd enjoyed the brief time he'd spent in Antarctica with the project. He'd spent a lot of time working with the scientists initialising Ancient tech and in the chair. The chair itself was a head-rush; the physical adrenaline burst of flying combined with a peaceful mental head-space that reminded him of sitting on top of a Ferris wheel; there had been a sense of rightness once he'd gotten over the terror of having so much power at his fingertips and something whispering in the back of his head to take it. He could have stayed in the chair for the rest of his life and been happy.

The scientists were a mixed bunch; Colonel Carter seemed the most sane and approachable although he understood from what he'd picked up from others she was the leader of the premier Stargate team and wouldn't be on the expedition. It was a pity but the CSO, McKay, definitely knew his stuff and John mostly found his loud berating of his fellow scientists amusing in a I-can't-believe-you-really-said-that-out-loud-even-if-it-was-true way. Working with him was going to be a challenge but John figured it was mostly going to be a fun challenge. He'd also agreed to allow his genome be used for gene therapy so he'd spent some time with the geneticist Beckett. He seemed like a nice guy; someone John hoped would be on the expedition.

He hadn't met many of the military members of the expedition beyond a young Lieutenant called Ford. It wasn't surprising. The military CO had been Stateside while John had been in Antarctica and then there had been the surprise vacation. John wished he could have met the guy before the day the expedition was scheduled to leave.

He repressed the urge to tug on his tie and focused on the floor counter. He was proud to wear them but he hated his service blues; he always felt too restricted in them; too buttoned down. He wondered if his duffle which he'd handed over to another Airman would find its way to the Pegasus galaxy or whether he'd be left without clean underwear.

He'd spent his vacation mostly on the West coast; as far away from his family he could get without leaving mainland America. He'd debated calling his brother; flipping a coin so many times he'd lost count. He'd debated calling his father but it had taken one coin flip to tell him that he didn't want to; was still too hurt and angry to have that conversation.

It wasn't a suicide mission, John reminded himself. He was coming back. It wasn't as though this was going to be his last opportunity to see them, and he didn't want to see them after what had happened the last time they had spoken; the angry words, how his father had blamed him for…John pushed the memory aside. He had to focus on the mission and he couldn't do that with his personal crap in his head. He'd told his father and his brother that they wouldn't see or hear from him again and he'd meant it. They certainly hadn't been in touch with him since. Maybe it would be better if he acted as though he didn't have family going forward. He took a steadying breath and followed the Airman off the elevator to the General's office.

O'Neill was on the phone but he waved John inside and dismissed the Airman efficiently with another gesture. The office was smaller than John had imagined for the guy leading Earth's forces against an invading alien enemy; almost cramped. Pictures of the General's time in service decorated the walls along with his educational diplomas. There was a dresser behind the General's desk; a comfortable leather chair, a couple of visitors chairs. There was also an internal window through to a briefing room which looked as though it had been converted into a mission control; computers everywhere with the room overcrowded with people.

The sound of the phone settling back into its cradle had John turning smartly back to face the General and correcting his posture. 'Major Sheppard reporting for duty, sir.'

'At ease.' O'Neill sat down with a bounce and pointed at a visitor chair; John sat. 'Firstly, apologies for the short notice recalling you and for the long wait you had for the final decision. This isn't ideal.'

No kidding, thought John. He'd spent three weeks surfing and fiddling his thumbs waiting on them making a decision instead of preparing for what was the most unusual and possibly the most important mission of his life.

'But you're smart and you're quick,' O'Neill smirked, 'I have every confidence that you'll catch up. And while we're not in the habit of sending people through the Stargate with no training these days…my team did it and survived.'

'That's very reassuring, sir.' John said dryly.

O'Neill's smirk grew. 'Yes, I'm sure it is.' He glanced up at a knock on the open door.

John followed his gaze and took in the sight of Doctor Weir in a cherry red top and a man in Marine BDUs wearing a glower on his face. His new CO, John thought with a sinking heart. He got to his feet and made sure to keep his posture parade perfect as O'Neill gestured for them to enter.

Weir held out her hand. 'Major Sheppard.' She smiled at him brightly. 'It's good to see you again. I can't tell you how happy I am that you'll be coming with us.'

John returned her smile and handshake a little hesitantly. 'Uh, thank you, ma'am.' He nodded an acknowledgement at the Colonel standing beside her. 'Sir.'

'Major John Sheppard, Colonel Marshall Sumner.' O'Neill motioned between them. 'Marshall, Major Sheppard.'

Sumner offered his hand and John took it. The contact was brief and brisk. Sumner's eyes skated over John's medals and widened a little. He hates me, John determined, and doesn't believe I earned them. It wasn't a surprise. Most of his COs hated him after reading his record.

'I'd like to sit down and hammer out the details of the assignment since Major Sheppard will be working for me.' Weir stared at Sumner pointedly.

'I would agree since there are military exceptions to that assignment.' Sumner replied with a calmness that belied the tension in his face. 'But we really don't have time for that today.'

Great; power struggles already, John mused silently. He shot O'Neill a look to see if the General had noticed. O'Neill met his gaze with a healthy dose of amusement so yes, he knew and he knew exactly how awkward it was going to make John's life. John would be irked but he guessed he had O'Neill to thank for the exception that he'd noted in his orders which said his primary duty would be piloting if they found flight capable spacecraft.

'Well, we'll have to discuss this on the other side.' Weir said brightly. There was a touch of steel in her tone that John had heard before in Antarctica.

'If we get to the other side.' Sumner countered.

'I guess I'll have to be the optimist in our team, Colonel.' Weir returned. She turned back to John. 'Did you at least get to enjoy your leave?'

John could see Sumner's disgust that John had been on leave out of the corner of his eye. He stiffened because the Colonel couldn't think John had been happy about it, could he? Or maybe he was just inclined to think the worst of John. Well, so be it.

John smirked deliberately. 'I did a lot of surfing.' He'd also read the stuff O'Neill had sent him and completed the personal preparations he'd needed to do in the hope he would be joining the expedition but Sumner didn't need to know that.

Sumner didn't hide his disgust at the word surfing. O'Neill let out a snort behind him. Weir's lips twitched as though she realised John was deliberately provoking Sumner and was amused by it. She probably was, John realised.

'Well, leave's over, Major.' Sumner said. 'We don't have anyone spare to babysit you this morning. I trust you can gear up and get to the gate without someone holding your hand?'

'I'm sure I'll manage, sir.' John said blandly rather than rise to the baiting.

'You'll need to stop by the infirmary and have a full physical too.' O'Neill said cheerfully. 'I think they want more of your blood before you leave in case we need to clone you.'

John's eyebrows shot up. Clone?

'Don't worry, just joking.' O'Neill assured him. 'Kind of.' He took in their small group in one glance. 'So I suppose I should say something inspirational but as I haven't had coffee yet, maybe we can all just get back to work?'

Weir smiled somewhat fondly at O'Neill. 'An excellent idea, General.'

Sumner nodded an acceptance. 'General.' He darted another dark look at John and made his escape.

'I can show you the way to the infirmary, Major.' Weir offered, motioning towards the open door.

'I'll take him. I haven't finished with him yet.' O'Neill said, stopping John from taking the step he'd been about to take towards her.

Weir nodded briskly although another unhappy look slid across her face before she replaced it with a more diplomatic smile. 'Of course. I'll see you in the gate room, Major.' She stepped backwards and disappeared.

John focused on O'Neill.

'Surfing?' O'Neill repeated dryly, one scarred eyebrow rising.

'Waves were great, sir.' John replied evenly.

'You're not going to make this easy on yourself, are you, Sheppard?' O'Neill got to his feet. 'Come on. Sumner was right about there not being a lot of people around to help you navigate the SGC today – we pretty much told anyone who wasn't needed to be here not to be here.' He sighed as he led the way from his office back to the elevator. 'Unfortunately, it turns out being a General means I'm needed.'

John smiled. He liked O'Neill. He wished O'Neill was coming with them instead of Sumner.

The elevator was surprisingly empty. John followed the General in and watched which floor he chose.

O'Neill pushed his hands into his pants pockets. 'For what's worth I will say that I think they're going to need you.' He looked at John seriously for a long moment. 'But you're not going to be able to save everybody, Sheppard.'

'I can try, sir.' The words slipped out before John could stop them.

O'Neill smiled knowingly. 'And that's why they need you.'

O'Neill got out of the elevator and John followed him down another corridor. He pointed at the door. 'Doctor's through that door. I'll get somebody to bring your gear up. I have to check on Carter and make sure she hasn't killed Siler or McKay for messing around with her gate.' He patted Sheppard's shoulder as he took a step back. 'My sage advice for what it's worth: trust your scientists. They'll be the ones who save your ass most of the time. Good luck, Sheppard.'

'Yes, sir.' John made a half-hearted effort to get into an 'at attention' pose as O'Neill sauntered away. As soon as O'Neill turned the corner, John immediately dropped the tension out of his frame and stared around at the concrete walls.

What was he doing? Aliens? Spacecraft? An expedition to another galaxy and the lost city of Atlantis? A military leader who hated him and who already had a serious power struggle going on with the civilian leader who John effectively reported to? This was going to be a disaster.

'Good going, John.' He berated himself quietly.

He took a deep breath and closed his eyes. OK, OK. He could do this. He'd out-flown an alien drone thing. He'd sat in a chair and conjured a solar system out of thin air. He had a mutant gene. He could step into a wormhole and explore a lost city in another galaxy. He opened his eyes again. It was time to leave his past behind and start his future.


Daniel sat in front of the whiteboard and stared at the text unseeingly. The Atlantis expedition had left hours before; left without him. The video images from the MALP had been fascinating showing an architecture that was startling and grand. It had looked like there were no Ancients in residence but they hadn't really expected to find any; all the preparations had assumed the city would be abandoned.

He wondered what the expedition was doing; how they were feeling. They hadn't made the contact time if they had been able to connect back to Earth so the prevailing theory was that the city must have lacked the necessary ZPM required for the dial up.

The expedition was stranded a galaxy away from home on an alien planet in an Ancient city.

The want – the need – to be there spiked through him sharply. He should have – what? Abandoned his team? Run through the Stargate behind the expedition with only the clothes on his back?

Daniel took off his glasses and pinched the brow of his nose. It had been a long couple of months. The weeks in Antarctica had produced the location of Atlantis but it hadn't been as productive in providing an answer to their Anubis problem. The project had unearthed a stash of drones but no other weapons; nothing else to help them.


It felt very much like failure.

There was something about Anubis – something that hovered at the back of his mind – some memory that nagged at him. It was like an itch in the middle of his back. No matter how much he squirmed and contorted to reach it, he couldn't. But Daniel was certain that it had something to do with when he'd been Ascended. Probably something to do with what had happened at Abydos with the Eye of Ra and the stupid, stupid deal Ascended him had apparently made to give Anubis the Eye.


But whatever it was, it was driving this need to defeat Anubis; to eradicate him from existence. The depth of that need scared him. He wasn't a pacifist. In the face of Ra he had encouraged the Abydonians to take up arms even the children; he'd hated Apophis for stealing his wife and hadn't been inclined to mercy; he genuinely believed that the Goa'uld as a species were nothing more than parasites who stole the lives of others and didn't deserve to live. But he didn't like violence. He preferred to talk his way out of trouble; preferred debate to solving things with fists and guns. It worried him that he could want someone, some living creature even one as vile as Anubis, dead that much.

So: failure. He hadn't discovered what he'd needed to in Antarctica and he hadn't gone to Atlantis to find it.

Sam appeared suddenly in his eye-line. She was dressed to leave in civilian clothing of a leather jacket over well-worn jeans and a blue sweater that Daniel knew Cassie had bought for her.

'Hey,' Sam said waving to recapture his attention from her sweater, 'are you OK?' Her blue eyes were brimming over with concern.

'Yes.' Daniel shook his head. 'No. I don't know.' He folded his arms over his chest and shrugged, dredging up a smile. 'I'm still here.'

Sam hovered for a moment and took the stool beside him with a sigh. 'You know I was going to talk to you about this in Antarctica and I chickened out.'

Daniel shifted to look at her, confused. 'What?'

'You wanted to go to Atlantis.'

'Yes.' Daniel agreed. He wanted to go to Atlantis; he'd never hidden that he wanted to go to Atlantis.

'Are you…' Sam worried at her lip and sighed again. 'Are you unhappy?'

'Unhappy?' Daniel repeated, blinking at her. Maybe he was more tired than he thought. 'Why would you think I was unhappy?'

'I don't know,' Sam said slowly, 'maybe because you want to leave and be somewhere else?'

He really was stupid.

'I promised myself when you came back that if you…if I thought you…' Sam stumbled through her words. 'I promised I'd talk to you if you were unhappy.'

Daniel turned to her hurriedly. 'I'm not unhappy, Sam.' He took her hand and tangled their fingers together. 'I'm not unhappy; I swear that…this is not that. I promise.'

Sam squeezed his fingers gently as she searched his expression. 'OK. So do you want to tell me what it is if it isn't that?'

He gave a snort. 'I'm not sure I know.' He sighed as he searched for the words to explain. 'I just have this deep down gut feeling that the Ancients knew the answer to defeating Anubis; that the answer is in Atlantis.'

Sam's gaze sharpened. 'Is this like when you knew about Bra'tac and Rya'c being in trouble?'

'Not exactly,' Daniel said, 'I'm not getting visions or anything. It's just…just a feeling.' He shrugged again, unable to explain it further.

'OK.' Sam pressed her lips together. He could almost hear her thinking. 'You know it's too surprising.'

'It isn't?' Daniel said surprised. He shifted round to look at her more fully.

Sam shook her head, the blonde strands catching the artificial light and gleaming gold. 'On Abydos, when we had the Eye and you appeared to us, you were absolutely convinced that the lost city on the tablet was the answer to stopping Anubis.'

'I was?' Daniel frowned. He'd heard about what had happened; had read the reports; had been told. But it was the first time someone had mentioned his certainty.

'Maybe,' Sam began tentatively, 'maybe your need to go to Atlantis is your subconscious trying to remind you of that.'

Daniel's fingers tightened on hers for a moment. 'Maybe.' He conceded. He breathed in deeply; taking in the familiar scent of books; of paper and ink that suffused his office. His eyes caught on his picture of Sha're. He jerked his gaze away. 'I know why we weren't allowed to go, I mean without a guarantee of getting straight back, and I know we're needed here, but…I just can't help but wish we'd gone with them.'

'We?' Sam asked, starting to smile.

Daniel nodded. 'What?' He frowned as something occurred to him. 'You thought I wanted to go alone?'

Sam raised one elegant eyebrow. 'Well, Doctor Weir might not have helped by campaigning to have just you join the expedition.'

He flushed. 'I didn't mean to…I mean, I'm sorry…'

She waved off his apology. 'Don't worry about it.' She sighed. 'It's probably more my problem really.' She ducked her head. 'I guess I've been feeling a little insecure about the whole leading thing. I mean, I haven't had the evaluation yet to confirm that I am the leader and…between that and Antarctica and helping the expedition get ready to go we haven't had much time as a team lately.'

'I guess not.' Daniel murmured. He squeezed her fingers again. 'You know Teal'c and I love having you as our leader, right?'

She blushed even as she rolled her eyes at him. Her gaze suddenly darted to the clock and she winced. 'I should get going otherwise Pete's going to think I stood him up again.'

Daniel swallowed down the urge to ask her how it was going with her boyfriend. He nodded and let go of her hand. She hugged him briefly before she slipped off the stool and made to leave.

'Sam?' Daniel stopped her just as she reached the open door.

She looked back at him questioningly.

Daniel got off his stool and shoved his hands in his pockets. 'Is…what you said about my wanting to leave like…like before. Do you think that's why Jack's been such an ass about my wanting to go?'

Sam's expression shifted from inquisitive to thoughtful to rueful. 'You should probably ask him, Daniel. He headed out about an hour ago.' She tapped the door jamb lightly and walked away.

Daniel grimaced. Talk to Jack. Right, because that was always easy. He sighed and his eyes drifted again to the whiteboard. Maybe he should email Aiyana's journal to Jonas the next time the wormhole was up between Langara and Earth. Jonas had a good grasp of Ancient and he had known Aiyana, had spoken with her. Maybe he would find something in the journal that meant something that Daniel had overlooked because he hadn't been around when they'd met Aiyana.

He hadn't been around.

Because Daniel had been Ascended; living on another plane of existence that had no interest in getting involved with the lives on the lower planes. Resentment at his Ascended-self surged through him again. He pushed it away and started to pack up.

It was a couple of hours before he found himself outside of Jack's house, dressed in jeans, a checked shirt and a warm coat. He rapped on the door and waited for Jack to answer.

Jack opened the door, barefoot and similarly dressed in jeans and a t-shirt. There was a beer in the hand not on the door. He beckoned Daniel inside, went to the kitchen and came back with another beer.

Daniel took it and sat down in the chair across from the sofa. The television was playing an old movie, it was on low, the sound barely background noise. Jack sat down on the sofa and put his feet up on the coffee table.

'Some days,' Daniel began, 'some days I see you in Hammond's office and have to remind myself it's your office now and that I'm not in another reality.'

Jack tipped the beer towards him. 'I have to remind myself of the same thing.'

'Really?' Daniel glanced over at him, frowning.

'There's been a lot of changes in the last couple of months.' Jack shrugged. 'It's going to take some time for them to seem real.'

'Is that why you didn't want me going to Atlantis? Another change?' Daniel asked, forcing himself to ask casually.

'Bad things happen when you go off on your own, Daniel.' Jack pointed him. 'Things like you getting kidnapped and shot at.'

'Not all the time.'

'Well, there was that time you saved Kelowna and got a life-threatening amount of radiation.' Jack retorted sharply.

Daniel leaned forward suddenly, hunching over, his elbows on his knees, the beer dangling between his clasped hands. 'Maybe you're right because I went off alone when I Ascended and that obviously ended badly since Anubis destroyed Abydos and all.'

'I didn't mean…you have to let that go, Daniel.' Jack said exasperated. He took his feet off the coffee table and sat up. 'I figured that was why you wanted to go to Atlantis.'

'Yeah,' Daniel took a drink of his beer, 'I still think the answer is there.'

'So they'll find it and bring it back.' Jack said. 'Or we'll go and get it if we don't hear from them soon enough.' He shrugged. 'Either way, you're needed here more than there, Daniel.'

Daniel nodded, accepting that Jack would never give him another answer.

They both fell silent. Daniel thought about the Atlantis expedition again; their first night in an alien city. He knew how that felt even if it had been a long time since he and Jack had taken that first trip through the wormhole.

'Do you remember that first night on Abydos?' Daniel asked eventually.

'Eating that alien armadillo and you accidentally getting hitched?' Jack took a gulp of beer. 'Yeah, I might remember that.'

'I keep wondering what they're doing, the expedition, I mean.' Daniel rested his head back against the cushion behind him and stared up the ceiling. The bottle was cold in his hand.

'You think they're eating armadillo and getting hitched?' Jack tossed back.

Daniel gave an unwilling laugh. 'God, I hope so.' His eyes met Jack's across the den. 'I wouldn't change that.'

'Me either.' Jack twisted the beer bottle in his hands and looked away. 'Well,' he smirked, 'maybe the armadillo, Chicken Man.'

Daniel laughed.

Jack smiled and raised his beer. 'To the Atlantis expedition.'

It was a good toast; one that needed to be made. He hoped that the expedition would be OK; that they would have explore and make discoveries; that they would come home. That they would find the answer he couldn't.

Daniel raised his own beer bottle in reply. 'To their adventure.'



( 4 comments — Leave a comment )
Nov. 15th, 2011 12:17 am (UTC)
Great update! :)

The view points that you portrayed we're interesting and wished they could have done a little more of that in the show - but you gave us "a second chance". Seeing the struggle between Weir and Sumner, McKay and Sam, Sheppard and Sumner. The dynamics!

Looking forward to the rest of the series!
Nov. 15th, 2011 10:37 am (UTC)
Thank you as always!
Nov. 15th, 2011 04:16 am (UTC)
Beautifully done. And yay! for extras :) I love how you weave the continuity of the show throughout these aftershocks - you know the characters so well - they all react as expected - you can see them! The gradual 'humanisation' of McKay - a lovely touch. Thank you!
Nov. 15th, 2011 10:37 am (UTC)
Thank you - glad you liked it!
( 4 comments — Leave a comment )




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