Disclaimer: Definitely don't own anything or anyone related to SG-1. ::pouts::

Summary:Novel-length fic. Sam returns after a long undercover mission with the Tok'ra and is shocked to discover what's happened to Jack in her absence. Sam/Jack, with some Daniel/Janet as well.

Timeframe:Takes place approximately around Season Three, goes AU from there.

Note:I starting writing this fic probably about a year ago, and it's finally finished so I've decided to post it. :) Since it's finished, the new chapters will come along quickly.


Chapter One: Since You've Been Gone

She was nervous. Major Samantha Carter of the USAF was nervous. She'd volunteered to work side-by-side with her father on a highly secretive Tok'ra mission, not expecting it to take an entire year to be completed, and now she was returning to her true home, the SGC, to finally reunite with her team, her family, and she was nervous as hell. They'd been out of contact for the entire year Sam had been gone, and she was scared they'd be upset with her, or treat her like a stranger. But she never would have expected what she was about to be told.

Sam and her father were treated with a warm welcome, like relatives that had been away far too long, as soon as they stepped out of the stargate. They were both dressed in the familiar beige attire of the Tok'ra. General Hammond, Daniel, and Teal'c were all there to greet them with hugs and smiling faces, but the one person she really wanted to see wasn't there. Trying to be somewhat subtle and not looking hurt about his absence, Sam turned to Daniel with questioning eyes. "Where's...Colonel O'Neill?" she asked slowly.

The suddenly somber expressions on Teal'c, Daniel, and even General Hammond's faces were enough to have Sam fearing the worst when no one answered her right away. "What?" Her eyes were immediately glassy with tears as she gasped and brought a hand to her face. "Ohgod... Is he-? Did he-?" She couldn't even choke out the words.

"No, no, no," Daniel frantically shook his head as he realized what she was thinking, putting his hands on her shoulders to calm her with a semi-reassuring smile. "Sam, Jack's alive." His voice was quiet now, her blue eyes focused on him, waiting for an explanation. "He's here, on base..." he glanced off to the side where Teal'c stood. He took in a steadying breath. "He just... He couldn't be here, in the gate room for your arrival,"

Jacob's brows creased as he stood beside his daughter, just as curious as she was about the whereabouts of O'Neill.

"Then," Sam began hesitantly. "Where is he? Why couldn't he be here? Is he in the infirmary or something? And where's Janet?" She realized she was probably sounding like a petulant child at this point, and should have been a little less emotional about her questioning of her CO's whereabouts, but right now she didn't care. She just wanted to see him. It had been much too long.

"Come, we can discuss this in the briefing room," Hammond stepped in, tilting his head and waving them from the gate room.


"Sam," Daniel started to explain after being prompted by the General. "Jack was injured about a month after you left for the Tok'ra mission. We'd acquired a new Goa'uld weapon to study, and found it to be something like our shrapnel grenades. Teal'c hadn't seen it before so we figured it was something new they learned from us." He grimaced slightly at the thought, took a breath, and continued. "A team of scientists were working on it off-world, and we, SG-1, were supervising to check on their progress." He took a deep breath, watching Sam taking in all the information, then forced himself to go on. "There was an accident. The grenade went off, killed two of the three scientists. Jack was nearby. He got hit with a blast of some kind of energy from inside the grenade, and took some shrapnel to his head and upper body." Daniel paused at the look of shock and fear that washed across Sam's face. "To make a long story short, the shrapnel was removed in surgery with a few other pieces in less critical areas, but that combined with the energy he was hit with had already caused significant damage to his brain."

The entire briefing room was quiet for a long moment before Sam sucked in a breath and looked toward Daniel again. "How bad?"

When Daniel ducked his head, General Hammond spoke up to answer for him. "Major Carter, Jack O'Neill is no longer the same man he was when you left on your mission. His memory seems to be intact, if not entirely at his disposal, but his behavior has been drastically altered."

Sam gasped softly and closed her eyes, fighting back tears. She felt her father place his hand over hers on the briefing table, his eyes settled on her for comfort. The news had obviously disturbed him as well.

Daniel spoke up again to finish telling Sam and Jacob about Jack's condition. "He seems almost catatonic at times, having to be told when to eat, sleep, get dressed, a lot of things. His current mood effects how much he does on his own as well. Jack's very dependent on us and has to pretty much be constantly supervised. Once in a while he'll act out physically, but mostly he's quiet, even robotic. He hasn't really said more than a few short words at a time since the accident, and responses of any kind are usually few and far between. But as far as we can tell, he seems to understand most things we can explain to him." Daniel silently wished Janet was there at that moment to explain this. She did know better than he did, being the doctor and all. But the archaeologist figured he'd heard enough about Jack's condition in the past year to relay information. "Physically, he's mobile, but it took a while to get to where he is now, and he's...not quite as agile as before. Maybe a little clumsy at times,"

"Will he get any better?" Sam choked out, her voice tight with emotion. Her mind was racing. How could all this have happened while I was gone? This doesn't seem real.

"Doctor Fraiser is unable to determine that at this point," Teal'c spoke up, adding his input for the first time since the briefing began.

Sam just nodded, her head down, still taking everything in. She chewed on her lower lip and rose her head to lock eyes with the General. "Where is he now? Can I... Can I see him?"

Hammond nodded slightly, his fingers intertwined over the table top. "Dr. Fraiser's looking after him right now. They're in his quarters."

Sam felt bothered that someone had to be watching Colonel O'Neill, a man she had always envisioned as independent and proud. It made her want to burst into tears.

"I think both you and Jacob should take a little while to rest and clean up first. Get yourselves down to the infirmary for your checks as well." the General looked between Major Carter and her father.

"Yes sir," Sam nodded, rising to her feet automatically. She gave Daniel a brief hug and a wan smile, repeating the process with Teal'c as the Jaffa got up from his chair.

As soon as she made it to the locker room, Sam dropped to her knees and broke down in sobs.


After showering and getting her standard medical check down in the infirmary, Sam had composed herself and was now walking down the SGC hallways with Daniel, dressed now in the familiar comfort of her old BDUs. They talked about Jack as they made their way to his quarters so Sam could see him.

"So, he was forced into medical retirement?" Sam asked.

"Yeah, instead of a medical discharge," Daniel nodded slowly. "The General wanted to let him stay around, though. He thinks it might help Jack's chances of recovery, you know, being around things and people that are familiar. I also think that Hammond's afraid what will happen to Jack if he's not here. None of us want him to end up in some kind of special care facility or even a mental hospital, you know?"

"I understand. And I agree with you; I think it's probably best for the Colonel too," Sam agreed quietly. She didn't even want to think of what it would be like if he wasn't around at all.

Daniel smiled a little.

Although it saddened her to hear most of this, Sam wanted to know more. She needed to know what Jack was going through now, what she'd missed. "Does he live here all the time? Did he lose his house?"

"No, he's just on base a lot. The General was given full control of Jack's estate. He uses the retirement and medical pay to keep Jack's house running and everything, pay for all his expenses. Teal'c's actually officially living off-base with him there. Sometimes he stays with me and Janet if Teal'c's off-world or something."

Sam's eyebrows rose and she poked Daniel in the side with a slight smirk. "You and Janet?"

"Yeah," Daniel looked a little bashful, his cheeks flushing faintly. "We, uh, we started dating not long before Jack's accident, and eventually moved in together." He smiled, then turned the conversation back on Jack, feeling a little embarrassed. "He likes being around Cassie. Janet thinks it's good for Jack because Cassie doesn't really treat him like there's something wrong, and she's comfortable around him. It's like he can sense that, like he knows she's okay with him and it puts him at ease or something."

Smiling a little, Sam listened intently to Daniel as he continued to talk to her about Jack.

They walked the halls in silence for a brief moment before the archaeologist spoke up again as he slowed his pace.

"Listen Sam," Daniel said quietly, glancing sideways at her as they turned down another hallway. "I'm not sure how Jack will react to seeing you. We haven't had to...well...re-introduceanyone to him that he hasn't seen since before the accident. I don't want to get your hopes up or anything, but there may be a chance that he doesn't recognize or remember you."

Sam had already thought ahead. She knew that brain injuries could be a difficult thing. "I know, I understand," She took a deep breath, still trying to steel herself for a visit with her commanding officer that she hadn't seen in a year, and just learned that he had brain damage.

"Okay," Daniel nodded as he headed for the VIP suites.

Brows knitting together, Sam reached out to grasp Daniel's arm as he paused just outside one of the doors. "This isn't his quarters,"

Daniel smiled briefly at her. "It is now. Since he's mostly here on base during the day, General Hammond gave him a VIP suite of his own."

"Oh," Sam nodded as he twisted the door handle and pushed it open. She took a deep, steadying breath and followed him inside. Janet was sitting in the desk chair beside the bed while Teal'c sat on the edge of the bed with Jack. For a moment, as Sam stared at him, it looked as though everything was normal like she remembered. Same tousled silver hair, same well-worn BDUs, same lean frame with lanky arms and legs. Then she took a closer look. His expression was mostly rather vacant, his deep brown eyes staring without interest at the chess board on the bed between him and Teal'c.

Daniel moved further into the room to get Jack's attention as Sam waved over at Janet with a wan smile. "Jack," he tapped his friend's shoulder, causing the man to look up at him slowly with his head cocked to the side. "There's someone here to see you. She's an old friend that had to be away for awhile, but she's back now," He pointed over at Sam, watching as Jack's gaze shifted slowly to follow his finger.

Sam was still nervously standing in the doorway. Her stomach was turning in knots, and as the mostly-vacant gaze settled on her, she feared he wouldn't remember. "Hello, Colonel," she waved with a tentative smile, then dropped her arm back at her side self-consciously.

Janet shook her head at Sam and smiled briefly. "Sam, try calling him Jack. He doesn't really respond to Colonel," she suggested gently.

"Oh," Sam tried again, noticing he hadn't reacted and was still staring at her. "Hi...Jack, um..." she struggled for words and smiled hopefully. "It's me-"

"Sam," the softly spoken word held such deep meaning to the other occupants in the room in such a way Jack wasn't even aware of.

Daniel's jaw dropped, his eyes wide with surprise. "That's right Jack, it's Sam," he then said excitedly, giving his friend a gentle shoulder pat.

Sam smiled widely, tears glistening in her eyes with happiness. He was staring at her with more focus now, and she began to step closer as he stood, but Daniel held out a hand to forestall her movements. "What's wrong?" she questioned, suddenly feeling as though he was trying to keep her away from Jack. She didn't even know why that upset her so much.

"Sorry," Daniel sighed softly. "He uh... He doesn't really respond well to strangers touching him," He felt bad as her expression fell.

"I wasn't going to touch him, I was just coming closer," Sam defended herself, looking to the side of Daniel to see if Jack was reacting at all. "And I'm not a stranger Daniel," she added softly with a bit of hurt in her tone.

"I'm sorry Sam, but you are," Daniel told her quietly. "He may know your name, but that doesn't mean he knows you. You've been gone a long time; it may even feel longer to him for all we know what's going on in his head."

Sam just nodded a little sadly and didn't move any closer. There was a space of about four feet between herself and Jack, with Daniel standing almost protectively at the older man's side.

What happened next surprised everyone. Jack touched Daniel's shoulder and lightly pushed him aside, then closed the gap between himself and Sam. He stopped right in front of her and continued to stare, seeming to study her every feature.

Her blue eyes were wide in surprise, but Sam didn't move. She wasn't scared, just a little nervous under his studious gaze. Her eyes locked onto his, and for a moment it seemed like a sadness passed through that deep brown, followed by recognition. She felt her heart suddenly beating furiously in her chest as he suddenly and slowly wrapped his arms around her, embracing her in a gentle hug.

Janet and Teal'c both stood with surprise evident on their faces. Daniel's jaw dropped for the second time in less than five minutes.

Sam felt the tears tracking down her cheeks as Jack continued to hold onto her, leaning his head down on her shoulder in the familiar way he'd hugged her on those rare occasions in the past. It was comforting, just like his hugs always had been, making her feel secure and safe, making her feel loved. When he slowly let go, only to turn around and go back to sitting on the bed and staring at the chess board like nothing had happened, Sam felt cold and unattached. She already missed his arms being around her.

Realizing that Janet, Teal'c, and Daniel were still all staring in shock, she hastily wiped the tears from her cheeks and looked to them with raised eyebrows. "Uh, was that a normal reaction?"

"Uh... No," Daniel responded, shaking his head.

"Indeed, it was not," Teal'c agreed.

"That was just about the completely opposite reaction he's had to meeting other people," Janet added, now turning to look at Jack.

"I'd say," Daniel was nodding now, his arms slowly crossing over his chest. "Usually he either doesn't pay any attention, or shies away completely," he answered Sam's unasked question as to what Jack's opposite reaction to meeting others has been.

"So," Sam took a deep breath. "That was good then?"

Janet was grinning. "That was very good."

"Okay, well," finding herself suddenly fidgeting, Sam waved a hand towards the door and began to fumble for the exit. Her emotions were pouring out in waves now, and she felt unable to remain composed any longer. This was still way too much to take in after being gone for a year. "I'm really tired, I think I'll go... Uh, I just gotta go," Sam mumbled hastily, turning on her heel and fleeing from the room.

Daniel ran a hand through his short hair as he watched her leave. He turned to Janet and Teal'c with a sigh. "Coming back after so long, I really doubt she was prepared for any changes this drastic," he said quietly.

Teal'c gave a nod. "Indeed. Something of this magnitude is difficult to accept."

"Let's give her some time alone, then I'll go talk to her," Janet said softly and somewhat sadly.