Stargate SG1 is somebody else's, probably MGM/Gekko Corp/Sci-fi, and I freely admit that whoever's it is, I'm borrowing their show and they retain all rights, etc

Author's Note: Sam/Jack pairing so please turn away now if you're not that way inclined. This story is set referencing the events of SGA's Season 5 'The Last Man' which includes a number of character deaths. Although that is an Atlantis episode, this story is very much set in the SG1 universe which is why it's posted here. Mention of adult situations and spoilers for most of SG1 and SGA.

There have been a few Atlantis episodes where I've watched and just thought the scenarios do beg the question 'where were SG1?' After all, if the universe needs saving, SG1 is usually around. That's not to take anything away from the Atlantis characters who are heroes in their own right but some stories do just prompt the question. Anyway, 'The Last Man' was one of those and so this came to me...I hope you enjoy.

Destiny

Part 1: Destiny Denied

Two months after John Sheppard went missing, and just over a month before he was due to take his long awaited retirement, Jack O'Neill watched as Samantha Carter paced his office.

'…and the worst of it is the IOA act like it's not our problem.' Sam waved her hands in a gesture that reminded him a lot of their friend Daniel Jackson. 'We're responsible for what's happening out there and we have a duty we just can't walk away from…'

Jack nodded patiently and wondered when she would be finished venting. It wasn't that he didn't like watching her; Carter had always been beautiful when she was riled up about something but it was late, and she had only come back for the IOA briefing which was the subject of her rant. In four more hours, she would be beamed back to the Apollo to return to Atlantis.

'We need a ship.' Sam said decisively, turning to look at him expectantly.

'Isn't the entire city a ship?' Jack remarked caustically as he leaned back in his leather chair and raised a scarred eyebrow at her.

Sam shot him a look.

Jack sighed. 'Tactically, I agree. If we're to make any kind of headway, you need a ship to run some guerrilla warfare stuff for you but the Pentagon isn't going to commit any more resources to Atlantis for the fight with a bunch of Wraith mutants that don't seem overly interested in coming after the city itself.'

Her shoulders sagged beneath her dress blue jacket and she sank into the chair on the opposite side of his desk wearily. 'I've been going on about it, haven't I? Sorry.'

'Don't be.' He reached across the desk and held out his hand. He was pleased when she slipped her hand into his.

Sam gave him an apologetic smile. 'You want to grab some dinner?'

'How about we head home and grab some take-out?' Jack countered. His eyebrows waggled.

Her smile turned into a grin.

They got to their feet simultaneously. Jack reached for the jacket he had carelessly slung on the back of his chair and shrugged into it as Sam reached for a briefcase she had discarded by the door. They walked out of the building shoulder to shoulder; close but not touching. Their entire professional life had been spent that way and even though they were married, they observed protocol in official environments. It wasn't until they closed the door on their Washington apartment that they discarded the uniforms in all the ways that mattered.

They made an attempt at eating and catching up on news; Cassie's medical studies and latest boyfriend, Teal'c's new grand-daughter, and whether Daniel and Vala were any closer to getting together…half an hour in and both of them were too aware of the ticking clock. Sam got to her feet and held out her hand; Jack took it and followed her into their bedroom.

Jack held her as she snuggled up next to him; his arm was around her shoulders, pulling her closer. She would soon be gone again. Her upper body was mostly on top of him, her head on his chest, tucked under his chin. Her fingers were absently drawing circles on his stomach, bothering him in a good way.

'Carter,' he said conversationally, suppressed laughter teasing the edges of his otherwise strict tone, 'keep that up and you'll be naked when the Apollo beams you aboard.'

Sam laughed. She stilled her fingers and he felt a moment's disappointment. She raised her head to look at him.

He read the love in her eyes and his free hand covered hers, bringing it to his lips to kiss the palm. He hoped she could see the same in his.

She sighed and laid her head down again.

He stroked a hand down her back. He could read her so well sometimes it scared him. He could feel her guilt swirling as though it was a living, breathing creature. She'd lost a lot of people since the Wraith Michael had begun his onslaught on the Pegasus galaxy – good people like Sheppard and Teyla. 'It isn't your fault.'

'Doesn't make it any easier.' Sam commented. She didn't ask him what he meant.

'No.' He agreed. He knew all about the regrets every commander had no matter what the assignment – whether it was on Earth or…elsewhere.

Sam raised her head. 'I need to get ready.'

He accepted the kiss she dropped on his lips and allowed her to slip out of his arms. He heard the shower running and got out of bed, pulling on jeans and a t-shirt, unaware and unconcerned that his short grey hair stuck up in spikes. He found himself absently picking up their clothing, gathering together the debris of the Chinese take-out they had picked up on the way home.

Jack was in the kitchen when Sam joined him. She was in full military mode; sharp pressed suit, gleaming buttons. His chocolate eyes glanced off the eagles she wore – his. Her blonde hair was tamed into a sharp chignon, her make-up perfect. She was placing the hands free ear piece and mike in place. He wondered briefly with some amusement whether he should salute. Instead, he turned back to the coffee pot and poured her a mug. She accepted it with a grateful and distracted smile.

Jack rested against the kitchen counter, hands in his pockets. 'You really serious about a ship?'

Sam's eyes flew to his, registering his own shift to military mode. She lowered the mug. 'I'm serious that we need to do something.' She looked at him directly. 'The humans in Pegasus are suffering because of something we did. It doesn't feel right to sit back and do nothing.'

'You're not doing nothing.' Jack pointed out.

'Doctor Keller's work on the virus is not enough,' Sam shot back, 'and taking in refugees, warning planets where we can…it's too passive. We should be taking the fight to Michael.'

Their gazes held for a long moment.

'You've been hanging around with Teal'c too long.' Jack commented.

Sam smiled at the mention of their Jaffa friend. 'Or maybe a certain silver haired General.' She responded dryly.

He accepted the statement with a rueful grimace. He looked at her. The determination written across her delicate features had his mind flashing back to an early SG1 mission; a young Captain Carter with blue eyes snapping in defiance at him as she reminded him of his obligations…

'Freedom from oppression stuff, huh?' Jack said.

She nodded.

He sighed and shifted his weight. 'I'll see what I can do but no promises.'

Sam smiled at him. 'You're my favourite General, you know that right?'

'Really. I thought it was Hammond.' Jack joked lightly.

She chuckled and shoved her mug on the breakfast bar.

'Or Landry?' He suggested as she hugged him.

She was laughing outright when he kissed her.

Jack buried his face in her neck, breathed in the scent of her.

'Apollo to Colonel Carter.'

He was close enough to the earpiece to hear the call. He drew back but didn't release her.

She raised a hand to her ear and pressed down. 'Carter, here.'

He watched as she listened and replied asking for a minute.

Sam disconnected and looked at him. 'I have to…'

'I know.' Jack dipped his head and kissed her deeply before he let her go.

She picked up her briefcase and tapped the hands free mike again. 'Carter. Ready for transport.'

Jack kept his gaze locked on Sam's through the bright flash of light. When it faded away, the apartment seemed empty without her.

o-O-o

Sam was surprised when Jack and the rest of SG1 showed up unexpectedly with the Daedalus. His retirement was only days away so she figured he must have wanted one last tour. She smiled welcomingly as her former team-mates beamed into the middle of Stargate Operations. 'General.'

'Carter.' Jack smirked at her.

She couldn't help noticing that he looked at home, relaxed in the black field BDUs as though they were still an every day part of his life instead of the formal dress he normally wore as the head of Homeworld Security.

'I have something to show you.' Jack continued, grinning.

Daniel shot Sam a sympathetic but amused look as he slapped a hand over Vala's mouth to stop her from talking. Teal'c looked smugly satisfied and the SG1 leader, Cameron Mitchell simply shrugged apologetically.

'Sir?' Sam replied nervously.

'Relax, Carter.' Jack nodded at the technician. 'Open a comm link to the Daedalus.'

'Yes, sir.'

'Sir…' Sam tried to interrupt and Jack held up a finger.

'Ah.' Jack kept his gaze on the technician who nodded in acknowledgement of the open communications channel. 'Daedalus, Colonel Carter and I are ready for transport.'

Sam felt the tell-tale buzz of the transport before she could protest. She rematerialised on the bridge of a ship but it wasn't the Daedalus. Her head snapped round to Jack questioningly.

'You need a permanent ship based out of Atlantis. So, if you want her, she's yours.' Jack gestured vaguely at the monitors. 'She doesn't exactly fly – we had to tow her, and most of the Asgard systems haven't been finished yet. You've got a lot of work to do to get her ready.'

'Not a problem.' Sam murmured. She looked around with glee at the half-finished consoles of the empty vessel. 'She's really mine?'

'All yours.' Jack confirmed. He swept an arm dramatically at the commander's chair. 'You want to try it out?' His chocolate eyes twinkled irrepressively at Sam.

She ignored the humour and held his amused gaze with a serious one of her own. 'Thank you. I know it couldn't have been easy convincing the Pentagon to give us a ship.'

Jack's eyebrow quirked but he nodded. He cleared his throat and shuffled a little. 'About that, Carter…'

It was her turn to give an impression of Teal'c, her eyebrow lifting smoothly.

Jack shoved his hands in the pockets. 'I'm not retiring.'

Her eyes widened and her guilt was instantaneous as she realised what they'd done; forced him into giving up his retirement so she could have a ship. 'Jack…'

'Hey.' He held her gaze firmly. 'I agreed to it because it was the right thing to do. Eventually this Michael guy's going to finish with Pegasus and come looking for us.' He broke eye contact to look around the bridge. 'We need a ship out here.'

'We?' She repeated confused.

Jack shrugged, a hint of a smile playing about his lips. 'I managed to negotiate a few conditions myself.'

Sam straightened her shoulders. 'Such as?'

He took a step toward her. 'Such as SG1 are now assigned to the expedition.'

Her mouth fell open. 'But…'

'You mentioned in your last report that Ronon's trying to get a rebellion going, right?'

Sam nodded. The Satedan hadn't felt comfortable on Atlantis ever since Sheppard had gone missing. He'd left a week before to organise a human rebellion against Michael.

'Well, who better than Teal'c to help him get started with that?' Jack pointed out. He took another step.

'Daniel and Vala?' Sam asked, folding her arms across her chest.

'Someone needs to focus on exploring the city. There's a good chance that we might be able to find something here that will help us.' Jack's third step brought him within touching distance of her.

'Mitchell?'

'He'll keep Daniel and Vala from killing each other.' Jack said wryly. 'He's seasoned.'

Sam nodded. 'And you?' She still thought of him as part of SG1.

'I have to go back.' Jack took a final step; they were inches apart.

She closed the distance between them and hugged him hard. Jack's arms fastened around her in response, pulling her closer. They allowed themselves a moment but only a moment. She eased back and he let her go.

'I'd better get started.' Sam murmured. Her mind was already skipping ahead, listing the systems she would need to get up and running first, the diagnostics she would need to run…who she needed to help her. She turned back to Jack as he reached for his radio. 'What's she called?'

Jack sighed. 'Phoenix.'

'Phoenix?' Sam pulled a face. 'Isn't that a bird that self-combusts?'

'And is reborn from the ashes, Carter, don't forget that.'

She gave him a pointed look.

'Actually, it was Teal'c's idea.' Jack explained defensively. 'Apparently, it's the name of some super-mutant cartoon character that battles other mutants.'

Sam's lips twitched as she listened as Jack radioed the Daedalus to transport them back to the surface.

'Still couldn't get them to go for the Enterprise then, sir?' Sam teased just before the transporter caught them and Jack could answer back.

o-O-o

Something wasn't right.

Jack rubbed at his chest and stared around the SGC briefing room. Nothing had changed in the last five minutes as far as he could see. He still had another seven months to go before retirement and he was still stuck in what seemed to be a never-ending briefing. Hank Landry who was chairing the meeting was listening with interest to Richard Woolsey, who in Jack's opinion was boring the pants off everyone else in the room; the slide presentation hadn't moved on any. The air conditioning wasn't working; Jack's once-crisp shirt was stuck to his body. The room was stuffy and beginning to smell faintly of sweat. But he was used to that. The noise of the usual Stargate operations continued on in the background; comforting.

But, something definitely wasn't right. He'd been in the field too long to ignore his instincts so he sat back and waited attentively. Thirty minutes later, there was a clatter of footsteps on the stairs and Walter Harriman headed straight for Landry. When the SGC commander looked directly at Jack, he felt a sinking sensation in his stomach. Uh-oh, Jack mused.

'Gentlemen, I need to confer with General O'Neill. We'll call you back in a little while.' Landry clasped his hands on the table. His harsh gaze prevented Woolsey from arguing.

Jack watched the others leave wistfully. He got to his feet and stretched as the last man exited. 'So what's going on?'

'Jack, you may want to take a seat.' Landry advised.

Jack froze mid-stretch and stared at him. There was compassion and sorrow in the depths of Landry's eyes. Panic began to stir in Jack's belly.

Landry got to his feet. 'Jack…'

'No.' Jack lowered his arms and pointed a finger at Landry. 'Don't. Don't you tell me that.'

'They say she got the crew to safety.' Landry said quietly.

Jack turned away. He marched to the internal window, shoved his hands in his pockets and stared sightlessly out at the Stargate.

'Colonel Carter went down with the ship.' Landry continued softly.

Jack's head bowed under the weight of the words; he closed his eyes. Not Carter. Not his Carter.

They were making progress in Pegasus; the guerrilla tactics were working…Ronon's rebellion was beginning to have an affect although they'd lost Ronon himself. He'd talked to her the previous day after her formal report was done…

'Sounds like things are going great.' Jack commented. He moved closer to the monitor on his desk. He hadn't seen her for weeks.

Sam made a face. 'Great is maybe an overstatement.' She leaned in herself and he could see the worry in her blue eyes. 'I'm a little worried about tomorrow.'

'You think it's a trap?' Jack asked bluntly. The thought had crossed his mind during her earlier briefing of the planned rescue trip to a world targeted by Michael and his army of mutant Wraith.

'Maybe.' Sam sighed. 'But it doesn't matter; we have to take the risk.'

Jack pursed his lips. He'd always hated the thought of her in danger without him there to watch her six. 'Carter…'

'I know.' She reached out and touched her screen.

He did the same.

Their eyes held; love passed between them without words. They'd never needed words…

She couldn't be gone. Not Carter.

'I'm sorry.' Landry's hand landed gently on his shoulder. 'Colonel Carter,' he cleared his throat gruffly, 'your wife was an extraordinary woman, Jack.'

Some weeks later as Jack fished off the small wooden dock of his cabin, only snapshots of memory came to mind of the hours and days that had followed Landry's words.

SG1 returning through the Stargate…Daniel's red eyes…Teal'c's shattered expression…Vala's tear-stained face…

Cassie's heart-breaking cry of denial as she lost the third woman in her life she considered a mother…

The funeral bathed in bright, golden sunshine that made the white headstone blinding.

Jack could remember Teal'c holding a weeping Cassie and Daniel's hand clasped tightly in Vala's. He had been peripherally aware of the Atlantis expedition members present; Rodney McKay, Jennifer Keller, Radek Zelenka and Evan Lorne, and Carter's brother and family stood off to the side.

He remembered solemnly watching as the empty casket was lowered into the ground – there had been no body to recover. The gunshots had been loud when they'd fired and they echoed in his head along with the scream from the engines of a trio of F302s – Mitchell's tribute.

The memory of a grief-stricken George Hammond handing Jack the flag replayed in Jack's head; how his hands had tightened around the fabric convulsively. He hadn't wanted it yet he had held it because it honoured her.

All the small moments of grief and loss suddenly seemed to collide in Jack's mind, in his heart. He wasn't aware of the keening cry slipping from his lips or the rod falling from his grip. He wasn't aware of sliding from his chair to land heavily on the wood of the dock as tears streamed down his face. He was barely aware when Daniel raced from the cabin to hold him, when Teal'c's hand landed on his shoulder in shared pain. He only finally and truly knew she wasn't with him any longer; that Carter, his Carter, was gone.

To be continued in Part 2