My version of Stephen's early and missing years.

Usual disclaimer, no rights to any characters portrayed.

MIT Campus 1976

Stephen Bartowski wasn't quite sure which way to turn, as the golden boy of the computing and technology circles around MIT and beyond, he was getting offers from every corner after he finished his various science, computing and engineering degrees and had all the fame and accolades coming from his achievements, but the problem was that while pretty much any technical challenge was an open book to him, when it came to dealing with people, especially manipulative people with agendas, he was clueless, little more than a child. That was probably why, brilliant man that he was, he jumped at the offer from the men who came to him with a proposal to move to California to do his post graduate work, running a secret project in ground breaking technology for the government at Stanford.

Stephen thought it was great, he was being funded to work on his doctoral thesis and delve into in exciting new fields, and he'd always wanted to see San Francisco and the West Coast, could his life get any better? So he packed up and moved across the country to California and the Golden Gate.

When he arrived and went to set up his labs at Stanford, reality came crashing down around him though, because it was a classified government project, he needed approval to talk to anyone about any part of it, anyone that he wanted to work with had to be vetted and cleared by the government before he could approach them, his living quarters and labs had to be locked down like a missile base, and he had to have security guards around him at all times. What had seemed like a dream at first suddenly seemed like a nightmare. The only thing about the whole situation that he couldn't bring himself to resent was Mary, she was the only woman on his protective detail and they'd implanted her as his lab assistant so that she was near him at all times when he was working. Mary was about his age, bright (she was actually competent to act as his lab assistant, which was a shock), interesting and nice (and she was sort of cute, which tended to distracted him sometimes), so working with and talking to her was the only part of this arrangement that wasn't a chore. What didn't make sense was the fact that she was with him all day in the lab, but she also got stuck with the overnight protection duties once or twice a week, she must have really pissed someone off to get overloaded with work like that. He could see how it was wearing her out, she did her best but she was only human, so that night when she fell asleep when she was supposed to be on guard duty, he just took her shoes off and made her comfortable (putting a blanket over her to make sure that she didn't get a chill). Well yeah, he had spent about half an hour sitting there watching her sleep, but she just looked so sweet like that, the controlled, guarded expression she wore most of the time in the lab was gone and she just looked like an innocent little girl, so sweet.

When Mary reported herself for falling asleep on duty, everything fell apart, about a week later the other guards escorted him to another site to meet that creepy black guy, "Deputy Director Graham", who informed him that to fix the holes in his security, it had been decided that Mary would move in with him as his live in girlfriend (easily explained as a work romance that had taken off if and when it came out), while the other agents would handle all the external security requirements. Stephen went ballistic at that, saying that he wouldn't let him run roughshod over their lives in that way, and refused to go along with the arrangement. At that Graham just shrugged, saying that if he wouldn't accept Agent Knutsson in that role he'd replace her with another female agent, but the arrangement itself wasn't negotiable. When Graham played that card Stephen backed down and agreed to go ahead with it with Mary, which somehow didn't seem to surprise Graham at all. He was informed that they were arranging secure off campus accommodations to make it less obvious around the university, but when he and Mary found out that their accommodations were going to be a one bedroom apartment and they'd be required to sleep together they refused, so Graham just played the same card (replace her with someone else) again to make Stephen (and Mary for some reason) buckle again.

Things were awkward at first BECAUSE they felt so comfortable together, Mary was there to do her job, but they felt like a real couple, so when they were relaxing together it just felt so natural and comfortable to put his arm around her. Whenever they realised what he was doing he (or she) would jump up and go somewhere else, so it was awkward. It was worse in bed, they'd start the night on opposite sides of the bed, but usually by the time they woke up they'd be cuddled up together, so getting untangled from each other to get out of bed was really awkward. As time went on that only got worse, as they'd sometimes wake up to find themselves kissing and caressing each other, and they'd hardly be able look each other in the eye at work. Eventually, though, they gave in to it, they obviously couldn't stop this, so it would hopefully make it less obvious at work if they embraced it at home where they weren't being watched (or so they were told).

When Mary found out that she was pregnant, it was a major panic, she reminded him of all the rules against what they'd done and that she'd be be forced to have an abortion and sent away, so they spent the next month or two coming up with a plan to stop that happening. Stephen was pretty sure he had the trump card that would get them through this, if the CIA didn't leave them together and let them have and raise their baby, he wouldn't complete their projects. He'd heard enough around the academic and government circles to know that he'd achieved far more in the areas that they wanted than anyone else could, so if he refused to work for them, they wouldn't get what they wanted, that would hopefully be enough to force the CIA to give into them. They set it up so that there were others present at the status meeting where Stephen planned to give them his ultimatum (they couldn't leave it any longer as Mary was starting to show and the secret would definitely come out at her next medical). Graham blind sided them, though, by NOT arguing, he just smugly acted as if he'd known all along and sent Mary to a CIA cleared obstetrician and wedding planner to smooth the way.

Six months later they were a family, they had a nice little house (which strangely enough didn't seem to take the CIA any time at all to get set up), they had Eleanor, their baby, with them in a corner of the lab so they could see her any time they wanted. Of course, the CIA ramped up their demands on Stephen but he didn't mind that much, he had the life he'd wanted. The biggest demand from Graham and the CIA was for a new technology that they'd codenamed the Intersect, this was to imprint information (and other things) into the human brain in a form that could be recalled and used by the host. The intent was to imprint agents with the necessary information to do missions without requiring the lead time normally needed for them to learn how to do the things the needed for the mission (essentially programming the brain to do those things instantaneously). He received another (secret) requirement from Graham for this technology that he wasn't at all comfortable with, to have the ability to imprint a persona onto the host to allow them to essentially become a different person, basically it was instant and complete brainwashing, obviously something that Stephen didn't want to be involved with. When Stephen raised the requirement to be able to completely remove the imprinted persona without harming the host Graham said that of course that would be necessary, but Stephen could see that he didn't care about that element at all.

Over the next couple of years, Stephen collaborated with a few others scientist and engineers on the Intersect project (as well as his other projects), most notably an English scientist, Hartley Winterbottom. Hartley moved across to America to work with Stephen on the project and together they made inroads on the processes needed to imprint and remove the information and programming, managing to get it up to the point where it was possible to do so without harm to the subject (though some of their early failures made Stephen refuse to continue until Graham assured him that the volunteers had all fully recovered with treatment, they'd been relocated under the auspices of witness protection afterwards to prevent any attention being brought on the project, but they were fine). A year and a half before their second child, Charles, was born, Graham demanded a demonstration of the persona imprinting capability and Hartley volunteered to be the subject, as he had every faith in Stephen and their work together. The imprinting went well, and Hartley immediately changed from the shy, sweet, Englishman that he was into the "Agent X" persona (a brash, bombastic Russian), that lasted for the hour's duration that they had coded into the program, then he suddenly zoned out and came back as Hartley, asking whether it had worked. Even Graham and the other government officials seemed impressed and they had a celebration that day.

Work on the Intersect project and other technology projects continued after Charles was born, and Stephen was forced to collaborate with some people that he really didn't want to, like Ted Roarke, his old MIT "partner" who'd tried to take credit for his work back at MIT. Stephen had to admit that Roarke did bring some things to the project, but he wasn't comfortable working with him, even less so having him around his family, but luckily by the time he was forced by Graham to bring Roarke into the project, Eleanor and Charles had started school, so they weren't around when he was, and Mary could take care of herself (as the cast that Roarke wore for five weeks after he grabbed her butt showed).

When Charles was nearly nine, Graham came back with an urgent requirement for the persona imprinting function to be ready for actually use, they needed to insert someone as a Russian arms dealer into Eastern Europe and the image had to be perfect, so an agent playing a role wouldn't be enough, the only thing that could deliver what was needed was the Intersect imprinting. Stephen and Hartley worked on the necessary changes to the program, and given that Hartley had buckled to Graham's coercion to be Agent X again as he'd already proved that he could handle it without trouble, they ensured that there were a number of contingencies to get him out of it, firstly, it was hard coded to finish after six months (the expectations given were that he should only need to be there for a month or two, three at most, but he would be in danger if he dropped out to himself while he was in the middle of that environment), and they implanted a number of manual triggers to exit the program. The last measure that Stephen added with Mary's agreement was to code a mild affection for Mary into the program to make it easier for her to get close enough to Agent X (or rather "Alexei Volkoff") to use the manual triggers to get him out of the program if nothing else worked.

When Agent X was implanted and he was sent to Russia, everything went wrong, Stephen and Hartley had tested everything multiple times before they proceeded, but somehow the software or data had been corrupted, because this Alexei Volkoff wasn't just brash and bombastic, he was a violent psychopath. Stephen and Mary tried to get Graham to cancel the operation and get Hartley (Alexei) out of there but Graham refused, saying that it was working perfectly, the new persona was working even better than the original would have in the role. Graham pointed out that they'd told him that the program was hard-coded to finish in six months, so he could be extracted them. They didn't like it, but as there was no way of getting anyone to overrule Graham they went with it. Another problem was that with this new persona, it would be harder for other agents to get close to him, so Stephen grudgingly agreed with Mary when she pointed out that she'd have to go over there and use the affection that they'd coded into the program to allow her to get close enough to Alexei/Hartley to protect him when he dropped out of the program. Stephen knew that Mary was good, but she was his wife, his love, the mother of his children, if it wasn't their friend Hartley he probably wouldn't have agreed, but it was, so he let her go off for two weeks to bring Hartley back.

As soon as Mary got there and managed to infiltrate Volkoff Industries she reported another problem, there were obviously other issues with the program (beyond the whole violent psychopath thing) because the "mild affection" for her that had been coded into it and tested was now a full blown obsession. Stephen wanted Mary to get out of there immediately but Graham said that she was in place and it would ruin the whole mission if she got out without Hartley. Unfortunately Mary had to agree, and pointed out that she could hardly get out of Alexei's sight now, so getting away before the program terminated would be difficult, so they had to wait for it to finish. When the end date for the program came and went without word from Mary or Hartley, Stephen went to Graham to find out what was going on, only to be told that apparently Mary hadn't managed to get the Agent X program to terminate, and on top of that Volkoff had reportedly been tipped off that she was CIA, but nothing had been heard from her since the advice of the tipoff came through. Stephen's world came crashing down around him, his wife, his children's mother, had disappeared (presumably killed by their friend Hartley under the Alexei Volkoff persona), and he was being told by the government to forget about her and just continue with his work.

Stephen did continue, and try to keep up appearances for Eleanor and Charles, but he couldn't accept that Mary was gone, he had to find her and bring her home, and Hartley too. They had moved to a bigger house around the time that Charles started school, and given that designs had been disappearing from the lab since people that Graham insisted on being added to the project (like Roarke) came on board, Stephen had made some secret additions to the house to allow him to work on and hide the more sensitive (and key) elements of his projects away from those he didn't trust. Given that it was just him left to look after Eleanor and Charles, he now only worked in the lab during the time that they were at school, but while he was supposed to be looking after his children, his obsession with finding their mother took him further away from them all the time. If he had been capable of stepping back to really look at the situation, he would have been heartbroken by what he was doing to his children, and at the same time incredibly proud of the way that his daughter took over looking after her little brother, even though he was only about four and a half years younger than her.

Without any official access to any government resources to hunt for Mary, Stephen made use of the outgoing ARPANET, as well as the MILNET, FidoNet and NSFNET to get the access he needed to hunt for information around the world. (It was relatively easy to get past the controls that existed in the early days, but even though the controls developed, so did he, so he was always a step ahead of anyone trying to keep him out of things.) He spent most nights trolling the world for any hint of Mary, going through systems and databases in hundreds of countries in his search. While this was going on, Stephen had to keep up appearances as far as working on the Intersect project went, and he was still trying to find a way to cancel the imprinted Alexei Volkoff persona so he could get Mary and Hartley out when he found her, so he spent a lot of time working on the Intersect and other projects at home.

Unfortunately Stephen was losing his focus as he tried to juggle chasing the constant fruitless leads on Mary and the Intersect development, so one afternoon when Charles was ten and at home after school he forgot to lock the door to the workroom with his home version of the Intersect imprinting setup (they hadn't found a better way to load (imprint) the Intersect image into the brain than to embed the data in images using steganography, and then bombard the subject with multiple images simultaneously to overpower the conscious mind and force them past it (repeating them at different instances to ensure that there weren't any holes in the code that was imprinted). With the available technology, the only way to do this was to have a large array of display screens in front of the subject to show these images at the same time. It would have been great to have one or two large, really high resolution screens that could do that, and hopefully they would be available one day, but for now a wall of display monitors was the only way to do it, and that was what was in the workroom at the house). The issue was that Charles wandered into Stephen's workroom that had been left open when Stephen ducked to get something else and had initiated the imprinting process for a full version of the Intersect that Stephen was working on. This was a much bigger version than the one that Hartley loaded to be imprinted with Agent X and Stephen thought for sure that he had destroyed his son's brain through his thoughtless actions, but Charles was OK, by every logic he should have been a vegetable but he wasn't, he was fine!

From that point Stephen double checked that the workroom was locked at all times (whether he was in there or not), and he had another priority, to work out how Charles had survived the imprinting process, and try to ensure that he hadn't been harmed by it. The only thing that stood out when he went over everything was that the activation codes weren't in what Charles loaded into his ten year old head, so it was a massive (incredibly massive) data load, but it wasn't actually interacting with his brain functions as yet. Once Charles had shown that it was possible to survive the loading the full image, and given that he didn't trust Graham or anyone else with the full version of the Intersect, Stephen decided to load it into himself and activate it so that he could make use of it. Hopefully once he got it working properly he could pare it down to something less dangerous and then palm that off onto Graham and the government in hope that they'd let him get away from all of that with his family.

When Stephen loaded the full version, he realised that it affected him more than it had Charles, but he was still functioning so he went ahead and activated it. When he activated the Intersect Stephen passed out for about ten hours, but luckily it was overnight and Eleanor and Charles were used to him locking himself away in the workroom all night, so they didn't think anything out of the ordinary was going on. He found that with the Intersect functioning he could access the information he needed to progress his projects, but he also realised that his links to normal life (and indeed sanity) were being stretched rather thin, and the more he used it the worse he got. He knew that he should deactivate it and hope that he'd recover, but he felt that he was already past the point of no return, and the only way to succeed was to go on with it. Due to that decision, after another two years of that Stephen had made inroads on the Intersect, but he knew his brain was deteriorating rapidly due to the overload from the Intersect, so he decided that the only way to protect Eleanor and Charles (from himself, or from having to see him as a mindless vegetable) was to go away until he'd managed to fix it, then he could come back to them.

He kept an eye on his children after he left, and could see how hard it was on them to think that they'd been deserted by him as well as their mother (he hadn't been able to tell them what she was a spy who'd gone off to save their friend and that he may have killed her), but he still believed that they were better off than they would have been, living with a crazy man. Eleanor was almost seventeen and he'd left what money he could with her to keep them going until he fixed this, they just needed to keep their heads down and stay off the radar from the authorities until the problems were behind them.

The problem, though, was that he couldn't find the solution to the Intersect issues, the best he could manage to do was to build a governor device to suppress the electrical impulses generated by the program and stop (or at least slow) the degeneration that was going on in his head. Given that he'd promised himself not to let them see him in the state he was in now, he didn't go back. He did try to keep his eye on them for a while, but after a few close calls with government agents (and after he'd engineered accidents for those agents to prevent them reporting back anything about the children), he'd decided that he had to stay well away from them to prevent leading the government (or others, he'd noted that some of the groups coming after him seemed different) to them, and perhaps getting them hurt.

From that time, Stephen kept moving, he maintained a few on-going safe houses that he shuttled between and worked out of, and a few years later when Eleanor had to sell the house to get the money they needed for Charles and herself to survive (Stephen had set up alerts so that he'd be notified if and when that happened), he arranged to purchase the house through some anonymous proxies, because the secret bunker that he'd had built under the house without the government's knowledge was his best resource. That bunker held all the records on his search for information about Mary (and everything else), and anything significant that he'd developed, so he'd been waiting or a chance to be able to quietly get the house back to recover those records.

Most of what Stephen was doing from then on was the search for Mary, he half heartedly looked into the Intersect issues from time to time in hope of finding a way of repairing the damage, and would build computers and other devices as and when he needed them to aid his search or deal with those who were pursuing him, but generally all he did was search for his wife.