Disclaimer: I do not own these characters or the shows from which they come from.
Chapter 1 – season 2
After SG-1's heroic defeat over Apophis, the stargate program was reinstated. They were on the planet for less than five minutes when the gliders arrived out of nowhere and started shooting the place up, they had to do an emergency evacuation of everybody on the planet to the SGC. Sam leant down to do perform CPR for one of the wounded, as soon as she try to attempt mouth to mouth her head snapped up and her eyes glowed.
Jack came up behind her and grabbed her to make sure that she made it back to the gate, when he went to grab the guy she was trying to help she told him "he's dead, had some kind of seizer bit his own tongue".
They then ran full pelt to the stargate in order to escape. Once they arrived at stargate command the iris was immediately closed behind them, Sam stood still on the ramp looking behind her at the stargate. Jack turned back to look at her surprised by the fact that she wasn't following him as well as the fact that she looked shaken up even though she had come out of worse in the past he decided to risk it knowing how angry she could get when her competence was in question he asked "you alright?"
"Yeah I fine"
That afternoon during the briefing Sam behaved strangely especially to Teal'c, then she acted even stranger to jack when she mentioned that she hadn't had her post mission physical yet. During her physical Janet didn't notice anything out of the ordinary, she did however mention that Cassie had been asking about her a lot lately and if she had time could she go and see her tomorrow at the academy hospital.
The next day at the hospital Sam stopped by to see Cassie, when she gave Cassie a hug the Naquahah Cassie blood and that in the blood of the symbiot in Sam reacted allowing Cassie to sense the symbiot in Sam. Cassie backed away in fear and Sam's eyes glowed and she moved towards her blocking her escape.
After the incident with Cassie the symbiot in Sam became more and more anxious to get of world as fast as possible. So she slammed open the locker room door and angrily asked Daniel and Teal'c what the holdup was and where jack was. The second after Daniel told her that he left them a message to say he meet them In the gate room.
In the gate room Sam was anxiously walk back and forth in front of the gate rearing to go, Daniel and Teal'c came in through the left blast door while jack came in through the right one without any gear saying "stand down campers were on a hold"
"Why?" Sam queered
"I don't know some computer glitch" jack then injected Sam with a powerful sedative which should of knocked her out completely.
"What the hell was that?" Sam shouted
Jack looked from Sam to the syringe to Janet and Hammond in the control room. Sam turned her head away then turned around to face jack and pointed her gun at him. Her voice changed to that of the Gou'ald
"open the stargate"
Daniel unsure of what was really going on said "jack what the hell is going on?"
An SF comes storming in and shoots Sam in the leg with a tranq gun, she quickly pulls out the sedative and points the gun at the guard.
Jack grabs the gun from Sam and she hit him, he went flying across the room as she pulled a grenade and pulled the pin out the tranqs went away and the side arms came out.
"open the stargate or we shall all die"
Jack screamed "don't shoot" then to reassure himself "Teal'c"
The SF said "I have a shot sir"
"and if she drops that grenade then what"
"let me go I must go"
"no ones goanna open that stargate"
She looked at him to contest to his statement when her eyes rolled back and she fell backwards, jack was able to grab hold of her hands as she went down he picked up the pin from the floor and put it back into the grenade.
The next day Sam was in the infirmary, jack had refused to leave her side after the Ashrak had tried to kill her. It turned out that the symbiot inside Sam was called jolinar and that she was part of the Tok'ra and that she was just hiding out in the nasian man because she was wanted by the system lords.
The symbiot scarified its life in order to save Sam although the process of the symbiot breaking down and being absorbed by Sam's system left Sam depressed and unresponsive, she wouldn't even face jack let alone let him touch her.
A week later and Sam was back to her usual self with two differences one was that she now had a alien protein marker and naquadah in her blood, two was that she had now moved in with jack or at least most of her stuff was there and she was practically always there when she wasn't working on base. Jack had even tried to persuade her to get an actual driving licence instead of commandeering his car and driving it illegally.
Unfortunately Sam's second mission back on duty went a bit haywire, by trying to help someone they accidentally fell victim to the wrath of a more technologically powerful race that sentenced them all to prison. There they met someone who had the ability to create an organic power source to get them home. However once they got to the SGC did they then discover that she was a Gou'ald and that she was imprisoned for creating a plague that killed millions. She was unfortunately able to escape through the stargate.
SG-1 didn't seem to be having much luck lately, during their next mission as a team they ended up in captivity again. Jack, teal'c and Sam were forced to work in the mines while Daniel got addicted to the effects of the sarcophagus. During their enslavement and after they had learned that Daniel was alive and using the sarcophagus, Sam began having flashes of the memories of Jolinar.
At home after Daniel went cold turkey, jack brought a subject with Sam that he had been meaning to ask for a while now.
"Sam?"
"yeah" she was reading a intelligence report about Gou'ald movements.
"will, ahhhh, I mean, arhhhhh, do you want to move in with me?"
Sam turned and looked at him "ohhh, arrrhhhh, ok, sure"
"sweet" then jack went back to watching the Simpsons and absentmindedly rubbing Sam's feet, while Sam went back to reading her intelligent report.