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.

Final Update: A big thank you to everyone who has reviewed and sent feedback on this story; it has been greatly appreciated. Rachel :)

Author's Note: This is a Sam/Jack UST story. Please turn away if you don't like the pairing. It takes place after Abyss in S6; there are spoilers for all Stargate episodes up to and including Abyss. There is a lot of angst for the couple but to explain why would give the plot away - you're just going to have to trust me.

Please note that the story is complete but will be posted in chapters. I hope you enjoy and reviews/feedback is always welcomed.

o-O-o

Rifts and Chasms

Colonel Jack O'Neill looked at his gaunt face in the bathroom mirror and slowly lowered the razor he held. Six weeks before he had staggered through the Stargate on the Alpha Site after his ordeal at the hands of the Goa'uld Ba'al and had been rushed back to the SGC. Getting captured by Ba'al hadn't been his idea. Hell, he hadn't even been in control of his own body when it had happened. He had been hosting Kanan, a Tok'ra symbiote, in what was supposed to have been a mutually beneficial arrangement; Kanan got a temporary host to relay important intelligence from his last field mission and Jack didn't die from some virus he had contracted in Antarctica when they had defrosted an Ancient. Some mutually beneficial arrangement, Jack mused bitterly. He'd been healed but at a cost of being tortured by Ba'al over and over. He was only thankful Kanan had left him before the Tok'ra had died.

His mind shied away from the memories almost immediately and his hand trembled slightly as he ducked the razor under the faucet and washed it before slipping it into a glass on the side of the sink. He ran a hand over his jaw, searching for bristles and was pleased when he found none. OK, he was showered and shaved; getting dressed was the next on the list. He made his way from the bathroom to his bedroom enjoying the familiarity of being back in his own home. He'd been there less than a week and was slowly getting used to being outside of the confines of Cheyenne Mountain. His release had only been agreed grudgingly and he was still not back on full active duty.

He sighed as he unhooked the towel from his waist and patted the few still damp areas of his body dry. He tried not to notice that his body was thinner than normal, little more than muscle and bone. He'd lost weight during his withdrawal from the sarcophagus addiction that had resulted by Ba'al repeatedly reviving him within it. Jack barely remembered the first week of his recovery; cold turkey was tough whatever the addiction and his had been a doozy. He knew he'd only gotten through for two reasons: the words of his Ascended friend, Daniel Jackson, telling him he would be alright and the care of his team-mate Major Samantha Carter.

He reached for his boxers slipping them on before he stuffed his legs into old faded cords. He would change into BDUs when he got to the mountain and he didn't feel the necessity to dress in something smart; he craved comfort. His mind wandered back to Daniel as he continued to dress. The younger man had seemingly died five months earlier having sustained a massive dose of radiation poisoning off-world. But he hadn't actually died; he had Ascended to a higher plane of existence where matter only existed as energy.

Jack didn't understand why Daniel had chosen the path he had and although he respected it was Daniel's choice, he missed his friend fiercely. The bond between them had grown strong and deep since their first mission through the Stargate almost five and a half years earlier and Jack missed the other man like he imagined he would miss his right arm if he ever lost it. Maybe that was why he'd seen Daniel during his time with Ba'al, Jack mused. Maybe it hadn't actually been Daniel but some figment of his imagination that he had conjured from his own need for a friendly face. Or maybe it really had been Daniel…six weeks after seeing the archaeologist Jack could no longer determine which it had been. He sighed and pulled on a jacket.

He briefly checked his appearance in the mirror before he left. In some ways, little had changed on the outside; same silver grey hair cut short, same square cut jaw, lines that tracked across his face and the same deep chocolate eyes. Yet it was the eyes that gave it away; they were more guarded than usual, shadowed with his most recent experience. It would fade. He knew that; hung onto that.

'I guess what I'm trying to say is…you're going to be alright.' Daniel said as Jack looked up at him from the infirmary bed. There was a faint white glow around the other man giving away his non-corporeal form despite the illusion of his human self.

'How do you know?' Jack had to ask the question; had to seek the reassurance.

'You're just going to have to trust me.' Daniel said.

'I can do that.'

And he could, Jack reminded himself as he shut the door on his home and pulled on his sunglasses. He climbed into his truck, started the engine and headed for the base. He sat back and enjoyed the ride; the truck was running like a dream. He suspected that Sam had worked the engine over during his convalescence when she had taken care of his house and vehicle. She had taken care of a lot. His thoughts lingered on the Air Force Major and despite the nagging thought that he shouldn't be thinking about her at all, he let them linger.

Sam had gotten him through the last six weeks. It seemed to Jack that she had an uncanny ability to be there when he needed her and to give him space when he needed it. Importantly, she understood some of what he had been through. Not the torture, although she had been through her fair share in the past, but the whole Tok'ra experience. Four years before, Sam had been taken over by a Tok'ra symbiote against her will. Jolinar had ultimately died within Sam, killed by a Goa'uld assassin. Sam had all the memories of her symbiote buried in her subconscious and could remember the terror of having no control over her body or her actions. With his own experience fresh in his mind and the confusion engendered by the small number of Kanan's memories that he did have, Jack's admiration for Sam had grown tenfold over the previous weeks and with it his deeply buried feelings for her had resurfaced.

His relationship with the Major was complicated. They were both Air Force officers and subject to rules and regulations. He was her CO; she was a junior officer under his command. He respected the hell out of her as another officer and he admired her as a person; she was a wonderfully quirky woman under the layers of competent soldier and brilliant scientist, and God knew she was stunning. He had never denied his attraction to her but he'd slid from an attraction to a beautiful blue-eyed blonde into love so easily he still had trouble pinpointing the moment when it had happened. Their team, SG1, had formed a close-knit bond in their first few years of being together that they all felt more like family than work colleagues or even simply friends. Jack had suddenly found himself caring a lot more than he should for Sam given their military relationship. The crazy thing was it was mutual. Or it had been.

Two years before, an alien device had forced them to admit their growing feelings to one another. The team had almost been disbanded because of it but they had both assured the SGC commander, General Hammond, that whatever their personal feelings, the mission came first and he had given them a chance to prove it. A few months later when Jack had shot Sam to force an alien entity to leave her body almost killing her it had brought home to both of them that they needed to step back from each other. Jack knew Sam had tried to move on; so had he. There had been a few dismal dates that hadn't gone anywhere; a relationship that had ended because he'd been away too much. In truth, Daniel's death had done more to drive a wedge between them then anything else; Jack knew he had withdrawn from Sam despite her obvious grief and need. He'd done the same to his wife when his son Charlie had died. But despite everything, his feelings for Sam hadn't changed and if anything the last few weeks had only strengthened them more.

He sighed as he drove onto the base and parked in his usual spot. He knew Sam cared about him but it had been two years since she had copied his form of words and admitted that she cared about him a lot more than she should. He had no idea whether she felt the same; whether her actions in the past month or so had been down to feelings that she had buried or whether they were simply the product of her sense of responsibility about what had happened; she believed she had convinced him to take the symbiote. The problem was she was partially right. He should probably talk to her about that, Jack mused reluctantly, or maybe he could just ignore it like he ignored his feelings for her. Jack made his way into the base; through the security checks and into the second elevator. He headed for the locker room, nodding absently to greetings on his way.

He was pleased that the room was empty as he started to strip. He reached for the standard issue green pants, black t-shirt and green over-shirt. He liked having the team in the same colour even when they were just on base. He shut the locker door with a clang of metal and made his way to the commissary. A quick glance confirmed that the rest of SG1 was already at breakfast. He grabbed a bowl of cereal and some juice before he joined them sliding into the seat opposite Sam, who smiled a welcome at him, and next to Teal'c.

The large, dark-skinned Jaffa greeted him with the usual minimal tilt of his bald head, the gold emblem of his former position as First Prime of Apophis glinting under the artificial lighting. Jack nodded his own greeting at his old friend and at the new member of their team, Jonas Quinn. Jonas smiled back at him across the table but Jack was relieved to see the smile was a little reserved. Maybe Teal'c's influence was starting to rub off on the other alien, Jack mused wryly. Jonas might look human but he hailed from Kelowna; the place Daniel had saved before his Ascension. In fact, it had been Daniel's actions that had ultimately prompted Jonas to defect to Earth.

Jack stuffed some cereal in his mouth. His relationship with Jonas was always edged with that knowledge. In some ways, Jack blamed Jonas for Daniel leaving them although he knew the reasons were much more complex than action A leading to decision B. Jonas had fought for his place on SG1 and Jack had acquiesced; he still wasn't quite sure why. Jonas had helped them save Earth; Jack had been under pressure to take a Russian; Jonas had wanted to be like Daniel and make a difference…ultimately Jack knew it didn't matter why he had decided to offer Jonas the chance, what mattered was that Jonas was part of SG1 and he was proving himself to be an asset. Not that Jack had any intention of telling him that, at least not for a while.

If his own relationship with Jonas was edged with wariness, Jack could see that Jonas was certainly settling into his relationships with the other members of the team. Sam was definitely taking a big sister role with the younger man; a little maternal affection mixed with the mischief of suddenly having a younger sibling to torment. It amused Jack to see that usually hidden side of her on show. Teal'c, on the other hand, was revelling in his status as wise mentor to the younger alien, advising him on the ways of the Tau'ri and generally taking him under his wing. It had been Teal'c who had mostly ensured Jonas's contact with Jack had been pretty minimal while he recovered from his torture and Jack was grateful for that. It was bad enough Sam had witnessed as much as she had, if Jonas and Teal'c had been present…

'So what's on the schedule today, sir?'

Jack's head jerked up at Sam's question. He cleared his throat. 'Oh, you know, the usual.' His current workload consisted of nothing more than attending mission briefings, reviewing all SG team reports and signing off on them. General Hammond had determined that it would keep Jack in the loop while the Colonel was on light duties, provide him with valuable experience and relieve his own workload. Mostly, Jack was finding himself secretly enjoying it but he was eager to get back out into the field. He was hoping the results of his latest psychological evaluation would finally convince their CMO to return him to full active duty.

Sam smiled sympathetically.

'What about you guys?' He asked waving his spoon around the table.

'Running tests.' Sam said.

Jack knew better than to ask on what especially when she was obviously giving him a break and not trying to confuse him with technobabble. His brown eyes slid to Teal'c.

'I am attempting to teach Jonas Quinn how to box.' Teal'c said firmly.

Jack's eyes widened and they darted to the younger man. 'Really?'

Jonas nodded as he popped another grape in his mouth. 'I find it fascinating. I can't believe it's a sport.'

'Maybe we should have a sparring session sometime.' Jack surprised himself with the offer. He'd surprised the heck out of the rest of the team too he noticed with amusement at the varying levels of shock in their expressions.

Jonas recovered enough to grin back at him. 'I'd like that, Colonel.'

Jack nodded. 'So, just boxing? Teal'c hasn't introduced you to any other Earth sports? Like hockey?'

Sam rolled her eyes.

'Hockey?' Jonas looked a little puzzled before his very swift brain returned the answer. 'That's the game with two teams, sticks and a puck, right?'

'And ice.' Jack added. 'You forgot the ice.'

'Ice?' Jonas frowned. He was certain the book he'd read hadn't mentioned ice.

Sam took pity on him. 'It can be played on a field or on ice, Jonas.'

'Oh.' Comprehension dawned across the young man's smooth face and his eyes twinkled. 'Fascinating.'

'It's better on ice.' Jack said defensively.

'Yes, sir.' Sam said soothingly.

He shot her a look and she smiled at him. He forgot what he was saying. He was relieved when a moment later an Airman stopped at the side of the table.

'Colonel O'Neill, General Hammond wishes to see you and the rest of SG1 straight away, sir.'

Jack looked down at the half-empty bowl of cereal and threw his spoon into it as he rose to his feet and indicated for the team to follow him. He was laid back about military protocol but his respect for General Hammond ensured he followed the usual form that an officer did not keep a General waiting. Sam grimaced but abandoned her own almost finished breakfast, Teal'c following suit. Jonas tried shovelling the last of his meal into his mouth as he got to his feet and ended up having to run after them to catch them up.

'Any idea what this is about, sir?' Sam asked as they entered the elevator and she pressed the button to take them further down into the mountain.

'Let's hope it's good news.' Jack said shoving his hands into his pants' pockets and rocking back on his heels.

Sam's eyes gleamed with sudden understanding and he was grateful as she began a conversation about an artefact SG9 had picked up, successfully diverting Jonas's attention. They spilled out of the elevator, along the corridor and into the General's office.

'Good. You're all here.' Hammond said getting to his feet, a smile lighting his round face. His pale blue eyes rested on Jack momentarily before sweeping across the other SG1 team-members. 'I'm pleased to let you know that SG1 has been cleared to go back on the mission roster.'

'Yes.' Jonas punched Teal'c in the arm enthusiastically causing the Jaffa to glare at the Kelownan.

Jack swallowed his smile. He figured that the Jaffa was already contemplating what form his retribution would take. 'That's excellent news, sir.'

Hammond nodded pleased. His gaze flickered to Sam. 'I know you have ongoing work that will need to be completed and handed on to base personnel so I'll have SG1 included in the mission rotation in forty-eight hours.'

Sam smiled gratefully.

Hammond smiled back. 'Colonel, if you could stay behind a moment?' He didn't wait for Jack's nod before continuing. 'The rest of you are dismissed.'

'Yes, sir.' Sam herded the other members of SG1 out of the office, closing the door behind them.

Hammond waved at the chair in front of the desk and sat down in his own. 'Take a seat, Jack.'

The Colonel reluctantly subsided into the proffered chair.

Hammond clasped his hands on the top of his desk and looked over at the younger man. It amazed him to see Jack whole and mostly recovered. Any other man would have folded after what had happened with Ba'al. Jack had picked himself up and was ready to throw himself back into the conflict again. Hammond wasn't fooling himself that the Colonel was over his experience. He had read the Colonel's own report, the doctor's and the psychological reports on Jack and knew there was a great deal of healing for the other man to do but he had determined Jack would do it best where he was most comfortable; in the field, leading his team. It had been the only reason why he had authorised the return to duty. He cleared his throat. 'I wanted to speak with you about an idea I've had.'

Jack nodded warily.

'You've done a good job with the mission briefings and debriefings over the last few weeks, Jack.' Hammond began.

'Thank you, sir.' Jack acknowledged the compliment even though he was wondering where Hammond was going with it.

'I'd like to make it a regular addition to your duties.' Hammond said.

Jack's face creased in confusion. 'With respect, sir, I don't see how if SG1 is back on mission rotation.'

Hammond smiled. 'I was thinking about scaling back the number of missions for SG1.'

'Oh.' Jack frowned.

'Obviously the number of briefings would also decrease from those you've been doing recently to fit in with your availability.' Hammond continued.

'Obviously.' Jack echoed. He cleared his throat noisily. 'May I ask why, sir?'

Hammond's small smile widened. 'There are a couple of reasons, Colonel. Firstly, I've enjoyed having the additional time in my schedule over the last few weeks.'

'Ah.' Jack nodded in understanding.

'Secondly, we have more SG teams than ever. There's no need for SG1 to maintain the schedule of off world travel that was necessary in the early years of the programme. I'm sure Major Carter and Jonas would benefit from having additional time to progress projects here on base and Teal'c could use the time working with the other Free Jaffa.'

'I'm sure that's true, sir.' Jack admitted a little unhappily.

'Thirdly, I'd like my senior field officers to become more conversant with the base operations. If this works with you, I'd like to roll it out to other senior SG team leaders.' Hammond concluded.

Jack repressed the urge to sigh. He could understand Hammond's logic. 'I understand, sir.'

'Good. Then I'll have the sergeant draw up a schedule…'

The alarm sounded.

Both men were out of the General's office and taking the stairs to the gate control room in an instant.

'Report.' Hammond said.

Sergeant Walter Harriman looked up at the General. 'We have an unscheduled off-world activation, sir.'

Jack turned slightly at the sound of footsteps on the stairs and wasn't surprised to see the rest of SG1 make their way to stand beside him. A technician made way for Sam to sit by the console.

'We're receiving IDC, sir.' Sam reported briskly. 'It's SG2.'

'Ferretti?' Jack asked frowning. He had overseen the briefing for the team's mission to P1X465 the day before. They were supposed to be conducting a mineral survey to confirm the original survey's report of a high level of naquadah on the planet.

'Open the iris, Major.' Hammond confirmed.

Sam's hand hit the palm reader and the iris slid open in with a sharp hiss of metal sliding on metal. They all followed the General down to the gate room. They entered just as the first of SG2 came through the wormhole and onto the ramp. It was Ferretti and his second in command, Brace. They were carrying another man between them. He was dressed in a tattered SG uniform and his long brown hair covered his face. He was obviously unconscious.

'We need a med team here!' Ferretti yelled.

Hammond motioned for the order to be carried out as Jack and Teal'c stepped forward to assist Ferretti and the other soldier. They gently relinquished SG2 of their burden and lowered the other man to the ground where Jack gently turned him over.

There was a sharp intake of breath behind him from Sam and Jack felt his own heart skip a beat in his chest as he recognised the bruised and battered man; it was Daniel Jackson.