A/N: This takes place seven years earlier than the first chapter when it comes up. This is also my first journey into the world of Stargate: Atlantis. So please be kind! IzzieStar has helped me refine this story, also helping with the writing.
"Damn IOA bastards. Always getting in the way of what needs to be done." was General Jack O'Neill's first thought whenever he saw those representatives from the governing body of the countries that knew about the existence of the Stargates. They were sort of the Internal Affairs of the SGC. They'd been trying to figure out whether they could control the nanites enough to use them for medical purposes. They'd said that there was someone had been rescued and had participated in the project. Unfortunately, the project had not been successful.
"So who is the lucky winner that's going into Witness Protection for being the guinea pig for your science experiment?"
"That is need to know General, and you don't need to know."
Losing patience, tapped his two star general rank insignia. He growled,
"You are using my people; I have the need to know."
They had a staring contest for about 30 seconds when the rep nodded his surrender.
"As you wish, General, I'll tell you who it is if you promise to behave in a civilized manner."
O'Neill relaxed slightly. The man smoothed his suit before saying,
"Before I tell you, you have to sign this confidentiality agreement to not tell anybody…"
O'Neill signed it without a second thought. He would learn later that he would regret that decision.
"Especially not anyone from the Atlantis expedition, General. You can't tell them anything about this person and anyone that may be with at a future date."
"Why, who's the person?"
"Come outside with me General, and you will see who it is."
He went with the rep from the IOA. Even though he couldn't see the man's face, he could practically hear the man's smirk. Once they got to the meeting room, he realized why the man had been smirking. The person going into witness protection was the now former leader of the Atlantis mission, Doctor Elizabeth Weir. She stood up when he came in. Her clothes seemed baggier than normal. If one looked closely enough and if you knew her really well, you could tell she was…
After a few seconds of disbelief, he turned to the IOA rep and motioned for him to leave the room. Before leaving, he said to Elizabeth,
"Excuse me Doctor Weir; I need to have a word with this man in private."
Quickly leaving the room and dragging the IOA rep with him, he found an empty conference room.
"You self-serving pretentious asshole, now I know why you don't want anybody to know!"
"You can't do anything about that now, you signed that form. So as long as you are in the Air Force, you have to obey it. And by the way she refuses to identify the father. Maybe an old friend could get it out of her?" he asked with an evil grin on his face.
"I am not going to ask her that, it's her business who the father is and no else's here or anywhere else for that matter. You guys in the IOA just want to make life for her more difficult than it already will be."
The man had a smug look on face. Until that is, O'Neill gave an order.
"Tell me where she's going to be staying." in a tone of voice that said that it was not a debate or a request. It was an order.
"She'll be in Sedona Arizona. It's big enough to have things to do, but small enough to be able to keep an eye on her surreptitiously."
"Is she going to have any kind of privacy?"
"As much as pregnant lady with tiny robots running around her system is entitled to, we aren't going to be putting too many bugs in the house."
"How many is not too many?"
"That is not of your concern, General. Now shall we get down to business?"
Glaring at the man, he held the door open for him and shut the door behind him quickly. When heard the man stumble and curse, he smirked.
When the details of Elizabeth's relocation were finalized and a Doctor had been briefed on Elizabeth's unique physiology in preparation for the birth, O'Neill stayed back as Patterson took an urgent call on his cell.
"You know, Doctor? I've never been to Sedona. Always wanted to visit though."
Looking at him for the first time, Elizabeth nodded her thanks with a tearful smile. The IOA rep returned to the room and put his hand out for O'Neill, which he accepted with a dirty look.
Three Years Later
Since General Jack O'Neill had taken his new job as the Head of Homeworld Security, his life had been going pretty well; he was his own boss and he'd finally got the chance to be with the woman he loved. There was one thing that played on his mind and worried him with distressing frequency though. And with this thought he took out a confidentiality agreement and pushed it in front of Sam as she was completing her latest mission report. Once she had finished reading it through, she looked up at him with confusion.
'What is this about, Sir?'
'Sign it and you'll find out. And can we drop the 'Sir'. We're not at work.'
She scribbled her signature across the dotted line and returned it to Jack who slipped it in to his jacket pocket.
'Are you going to tell me what this is about?' Sam asked.
'A couple of years ago I had a visit from an IOA rep, said he had something to show me, turned out that it was Elizabeth Weir.'
'That can't be possible – she's dead, I was there when it was confirmed.'
'Well it is possible – I've seen her, somehow they managed to rescue her. God knows, maybe it was them who planted the clone.'
'What does the IOA want with her?'
'Not just her actually; Elizabeth's a mother now.' Jack said, raising his eyebrows.
At this, Sam's jaw visibly dropped slightly, 'Still, what use could she be to the IOA?'
'They're pretty interested in Elizabeth's robotic self-healing abilities – you know cure cancer, that sort of thing. Next on the list, world domination.'
Sam smiled at him, 'and what about the kid? Who's the father?'
'Kids, plural, actually. I have my suspicions, but I wouldn't mind a second opinion.'
Despite it being made clear to him that there would be repercussions if he did attempt to contact Elizabeth, he'd managed to make his way over to Sedona a couple of times now – the knowledge that his friend was completely isolated too much of a pull for him to ignore – and Elizabeth had worked out where in her house was bugged within about an hour of living there, so he was pretty sure that it was safe to take Sam.
About two days later, they were parked outside a small, nondescript house, the garden littered with toys. They made their way up to the house, from which they could hear Elizabeth singing a nursery rhyme, and rang the bell. The singing stopped and they heard several locks being undone before the door opened to reveal a surprised Elizabeth.
'Come on in. I'll be down in a minute.' She whispered.
Then, in a sing-song voice, she said, 'No, I'm not interested, thank you.'
Sam looked to O'Neill in confusion, but he put his finger to his lips and guided her downstairs to the basement, which had a personal touch that no other room in the house had, with several comfy sofas and photographs of the friends she could no longer see.
'The only room in the house that isn't bugged – I don't think they were counting on Elizabeth's interior design skills. That was what the whole 'thank you' thing was about – she has to cover up who was at the door so they don't get suspicious.' O'Neill explained.
'How can they treat her like this? She's a good person – there are people out there who miss her and would love to see her again.' Sam said.
O'Neill squeezed her hand as they heard footsteps coming down the stairs, the light gradually revealing a three year old on each of her hips. As the light finally hit their faces, and more importantly their hair, Sam gasped.
'Colonel Sheppard is the father?'
'See, that what I thought too.' O'Neill said.
'Yes, John's the father.' Elizabeth said sadly.