Title: Trojan Horse

Author: ReganX

Summary: "After all the trouble they went to to save the future of humanity, it's scary to think that one person could doom us all."

Spoilers: This story is set during Season Three of 'The 4400' and what would have been Season Ten of 'Stargate: SG-1', so anything up to that point is fair game, spoiler-wise, although it should be considered an AU of both shows.

Rating: PG-13/T

Feedback: Feedback is more than welcome, flames are not.

Disclaimer: I do not own 'Stargate: SG-1', 'The 4400' or any of the characters associated with either show.

Author's Note I: This story picks up a few days after the end of 'The Enemy Within'.

Author's Note II: For those of you just joining us, I would recommend reading the first two stories in the series ('A Life Interrupted' and 'The Enemy Within') to fully catch up, but here's a very brief recap of previous events; basically, Sam is one of the 4400. She disappeared on August 21st, 1998 – during the Season Two episode "Secrets" – and returned on August 14th, 2004. Her abilities are telekinesis and technokinesis. While she was sick as a result of promicin inhibitor poison, Sam was contacted by a member of the group of people from the future, who were responsible for the abduction of the 4400, and she learned about the part she was expected to play in protecting the future of humanity.

Chapter One

October 13th

A civilian in command of the SGC.

Jack hadn't thought that he would ever see the day. It wasn't that he had anything against civilians, or anything, but he had never expected that the Air Force would ever agree to turn one of their most vital commands, if not the most vital, over to the control of a civilian, let alone a civilian with no experience of working on a military base.

There was no doubt in his mind that this was a political appointment, but who was it who had wanted Dr Elizabeth Weir in command of the SGC, and why? General Hammond had indicated that the President was looking towards the future, when the Stargate Program went public, and wanted the SGC to be led by a figurehead who was known internationally and who would present a friendlier, more acceptable public face than a military general would.

"I've heard of her." Daniel seemed to be one of the few people at the SGC who knew anything about their new boss and he filled the rest of the team in on what he knew as they gathered together in the commissary for breakfast. "She's an expert in international politics. She mediates top level negotiations for the UN. I'm surprised that you haven't heard about her, Sam," he added, "her work on behalf of the 4400 is well known."

"The name's not ringing any bells."

"She was the one who coordinated the international claimants in the class action suit brought against NTAC, the one that forced them to release you guys from Quarantine in the first place. She was also instrumental in putting together the international Charter of 4400 Rights," he said, referring to what had been a very controversial international agreement put together after word of the first 4400s to develop powers had become public news and concerns had been raised about military exploitation of those abilities.

"She didn't have anything to do with the inhibitor, did she?" Jack asked suspiciously. Since the full story had broken about the promicin inhibitor, and the number of influential people involved in it, Jack had been even more pissed off about it than Sam – and considering how angry she was over the whole thing, that was saying something.

"No, there hasn't been any indication that she even knew about it. It was all Dennis Ryland and his people. Even most of the doctors giving the shot never knew what it was."

"Or so he's saying." Jack muttered sceptically.

"Janet didn't know." Sam pointed out.

Walter entered the commissary, scanning the room and, spotting SG-1, he hastened over to their table and addressed Mitchell. "Excuse me, sir, but Dr Weir asked to see you in her office."

"What have you been up to now, Mitchell?" Jack asked in a long-suffering tone.

The other man grinned good-naturedly. "I guess I'm about to find out, sir." He responded, excusing himself and following Walter out of the commissary.

"The trial of Dennis Ryland begins today, does it not?" Teal'c observed, seeing the serious expression on Sam's face and the mention of the inhibitor and guessing the cause.

"Yes." Sam nodded confirmation.

"The son of a bitch is going to get what's coming to him, Carter, just wait and see." Jack said encouragingly. "He's going to rot in jail for a long time."

"I wouldn't be so sure about that, sir." Sam responded grimly. "There was a poll on TV last night – ninety percent of respondents believed that Ryland was right to do what he did. He nearly killed us – he did kill twenty-eight of us – and they believed that he was still right to try!"

"Well, the ten percent who aren't idiots still know that he was wrong, and when the rest of them come to their senses they'll realize it too." Jack said in a calming tone, noticing her use of the word 'us' but deciding against calling her on it, especially when she was already angry.

"He's right, Sam," Daniel agreed, "it's a lot for people to get used to, that all of the 4400s are going to have powers, and the idea of that change frightens them but once they get used to it, they'll realize that you were given your powers for a reason and that Ryland was wrong to try to interfere. You'll see."

"Before the trial?" She asked pointedly, knowing that none of them could promise that people would see sense so soon, or that the demonstrations in Ryland's favour wouldn't secure him an acquittal, despite being responsible for the deaths of twenty-eight innocent people, each of whom had had a part to play in ensuring the survival of the human race.

They ate their breakfast, in silence save for an occasional remark, for a few minutes until Mitchell returned and took his place at the table, a rather dazed expression on his face. He didn't say anything as he sat down, picking up a piece of toast but he didn't eat anything.

"What the Hell did she say to you?" Jack demanded, wondering what could possibly have stunned his second-in-command into silence.

"I've been transferred off SG-1."

Those five words were greeted with stunned silence, which was finally broken by Daniel.

"She can't do that!"

"She's in charge now, Daniel." Jack reminded him impatiently. "She's within her rights if she wants to shuffle the teams, or to have people transferred away from the SGC altogether. Has she said which team you're being transferred to?" He asked Mitchell.

"She's given me command of SG-3." Now that the initial surprise was wearing off, Mitchell was starting to see a silver lining to the cloud. He loved being a member of SG-1, and had learned a lot from each of his friends during the two and a half years he had been on the team, but he couldn't deny that the idea of having his own command had its appeal.

"But they're Marines." Daniel objected, looking from Jack to Sam before turning back to Mitchell. "If you're in the Air Force, can you even be in command of Marines?"

"Yes, but it's not usually the norm." Jack answered, wondering exactly how much Dr Weir knew about the ins and outs of a military operation – and why she seemed to be so determined to make splitting up SG-1 her first official act. "Excuse me." He said curtly, rising and leaving the commissary to seek out the new commander of the SGC.

"You know, that could definitely be an upside." Mitchell remarked as Jack left, a slow grin spreading over his face. "I'll get to order Marines around!"

Her new office was far smaller and far more Spartan than those she had been accustomed to over the past few years. Her predecessor had cleared out his things in preparation for her arrival, leaving the shelves and the walls looking bare.

It was certainly not an inviting room, Weir thought, as she surveyed her new domain, noting the large window looking out over the briefing room. If she left it open, then anyone who passed by would be free to look in on her, and she could forget the idea of having any privacy but if, on the other hand, she chose to close the blinds, it would look very forbidding, as though she was shutting herself off from the base she was supposed to be running. Once she had placed her own books on the shelves, some pictures on the wall and some personal ornaments on the desk it would make a difference, but this office was never going to be what she would call a comfortable place to be.

She knew full well how important appearance and body language were, but this assignment was completely unlike any of her previous ones and she was feeling out of her depth, something she didn't want her new colleagues to pick up on. She had decided against having the base personnel assembled for a formal introduction, deeming it impersonal and, knowing that she would soon come to know those she was working with even without it, she felt it was better to get to know them on a one to one basis.

"Enter." She called in response to the loud and insistent knocking on her door. "Colonel O'Neill." She greeted when the man entered, thankful that she had a good memory for faces and that she had read through the files of the senior officers.

"Dr Weir." He nodded briefly, but didn't take a seat when she indicated that he should do so. "I need to talk to you."

"About what, Colonel?"

"About the fact that you're dismantling my team without consulting me." He stated, without beating about the bush. Jack had been through this business before with Bauer when he had temporarily taken command of the SGC and he had no desire to repeat the experience.

"There's a big difference between one transfer and splitting the whole team, don't you think?" She observed in a carefully neutral tone, watching his reaction closely as she spoke, noting that he stiffened slightly at the mention of the possibility that the whole team could be separated.

"Is that the long term plan?" The question was blunt, but his tone was more restrained than it had been before.

"It's not."

Long experience of diplomatic negotiations had taught Weir the importance of masking one's emotions and she had to inwardly applaud the poker face of the man standing before her. All she had heard of Colonel O'Neill indicated that he was a man who cared deeply about his team and that he would fight to keep them together – she had been able to gather that much from his willingness to challenge his new commander over her decision to transfer a member of his team away – but once she had alluded to the idea of Major Mitchell not being the only one to be transferred, he had tried to keep his emotions and his temper in check.

"There were some concerns about the concentration of experience and expertise on SG-1," she told him, sparing him the discomfort of having to ask, "and as SG-3 was without a leader, having two experienced majors on one team seemed senseless. I understand that Major Mitchell has seniority over Major Carter, and your own evaluations have indicated that he is an excellent officer, so he seemed an ideal candidate for the vacant command position, don't you agree?"

Jack nodded slowly, unable to fault the logic of her decision. Mitchell, like Sam, was an excellent officer and he had never expected that either of them would be left on the team under his command indefinitely. When SG-3 lost their commanding officer, General Hammond would probably have looked to one of the two majors on SG-1 for a replacement, and it was very likely that he would have made the exact same decision that Dr Weir had made, so why was he so irritated?

It wasn't until he had actually left the office that it struck him; General Hammond would have spoken with him first, as a courtesy even if he wasn't actually seeking his permission, or even his opinion about whether he should offer command to Mitchell or to Sam. Dr Weir had made her decision, and hadn't even told him, leaving him to find out from Mitchell and, as far as he was concerned, that was not a good beginning.

Weir waited until he had left her office before exhaling softly, wondering what exactly she had gotten herself into.

When she had first been chauffeured to the White House, ushered into an office and told of the job she was being offered, she had been convinced that it was somebody's idea of a joke.

An ancient device discovered in Egypt that allowed people to be transported to planets all over the galaxy? A race of parasitical alien beings that used humans as hosts and who assumed the roles of the gods of Earth mythology? Mechanical blocks that formed into deadly bugs, led by a woman crafted from microscopic metal blocks? A secret command that had already stood between the planet and total destruction several times?

And they expected her to assume leadership of it?

It was no exaggeration to say that she had had some serious concerns about the President's sanity when he had told her that.

"The position was vacated very recently, and you were the best person I could think of for the job." There was no doubt that President Hayes could be a very charming man when he so chose and he had hit her with the full force of that charm when he was coaxing her to take the job.

"What happened to their last commander, General Hammond?" She had half-expected to hear that he had been killed, but what she heard was even more surprising.

"After he called General Bauer... some less than diplomatic names, I had to ask him to retire."

"Retire?" That had surprised her, given what she knew of the military. "He's not in prison for insulting one of the Joint Chiefs?"

Hayes shrugged. "He's an old friend – and it's not like he said anything that everyone who's ever met Bauer hasn't wanted to say at some point or another." As she had had the displeasure of meeting General Bauer, she could appreciate that. "So what do you say? Can I count on you?"

There had been little she could say to that save 'Yes'.

She may not have asked for the job, but she had it, and she was going to do the best she possibly could with it.

Strictly speaking, they shouldn't have been allowed to watch television while on duty, but under the circumstances, Jack gathered his team – including Mitchell, who he still considered to still be a member of SG-1 in everything but name – in his office to watch the coverage of the hearing, knowing that it wasn't just Sam who needed the closure of seeing Ryland get what was coming to him.

Given that he was being investigated for the part he had played in the deaths of twenty-eight people, one would have expected Ryland to be nervous and remorseful, but he spoke calmly, with measured confidence, as he explained the rationale behind his decision to institute the inhibitor program.

'The son of a bitch doesn't even think that he was wrong to do it!' Jack thought in disgust as he watched.

"The world has changed." Ryland stated flatly. Sam got the distinct impression that he was speaking as much for the benefit of the cameras in the room, and for the millions of people who were watching coverage of the hearing, as for the panel who were to determine his degree of culpability. "Everything is different now. The Promicin Inhibitor Program was an international effort. Its goal was to prevent the coming of a world dominated by a tiny fraction of the population. In short, we were doing everything we could to prevent the 4400 from developing extra-human capabilities. We believe that without the inhibitor program, these abilities would show up in virtually every one of the 4400."

"I don't believe this!" Mitchell muttered, disgusted by what he was hearing. "He's not even trying to deny what he did."

"Dennis Ryland's part in the Promicin Inhibitor Program is too well documented for him to entertain any hope of being able to plead ignorance, or to claim that he was not aware of the extent to which it was used worldwide," Teal'c observed logically. "His only hope is to persuade others that his efforts were necessary, and that his decision to initiate the program was the right one."

"And he seems to be doing a pretty good job of it." Sam commented bitterly. Ryland was playing on fears that had existed since word of the extraordinary abilities the 4400 had been gifted with had first become known to the public, and people were responding.

"I don't think I need to explain to this committee why that would be something less than the best-case scenario," Ryland continued, his tone bordering on self-righteous. "Overnight, normal human beings, like you and I, and all the institutions we've come to rely on would be obsolete. The program wasn't perfect. People got sick. Some died. That was not our intent."

"Yet they didn't come clean about it, even when everyone started getting sick or when they knew that it was killing people." Daniel remarked, scowling.

"If people like Dr Burkhoff had known what the problem was straight away, we'd have had a cure sooner, and lost fewer people." Sam agreed.

"But now it's gone." Ryland stated flatly, as though this was something to be sorry about. "And the future we were trying to prevent is here, and we are not ready. I believe it comes down to a question of power. Who is going to hold it? Us or them? Because, believe me, it's going to come down to us against them."

And that was it, Sam thought. Ryland had drawn a line between the 4400 and the rest of the population, dividing them into two distinct groups and setting one group against the other.

"People are going to see through that crap, Carter." Jack tried to reassure her.

"I'm not so sure, sir."

"Every day, the 4400 are changing and getting stronger. Instead of mobilizing to meet this challenge, we're wringing our hands and trying to determine who knew what when." Ryland continued, effectively turning those investigating him into the bad guys of the situation, "I will save this committee the trouble and expense of a long investigation. The inhibitor program was my idea. I was proud to lead it." He gestured towards a chart, with the pictures of the six men named as his chief co-conspirators. The men on this board were simply following my orders. If there's blame to be assigned, it's mine. Mine alone."

Sam was seriously tempted to turn off the television, if only to spare herself the irritation of having to listen to Ryland's rhetoric as he justified his actions but her need to see how the hearing played out won, and she watched as the one of the members of the committee quizzed Ryland over his insistence that he and he alone had been responsible for the program, that there had been no approval at a higher level.

If there had been, it was unlikely that they would never find out.

Ryland's words were interrupted by a steady whine, like feedback from a microphone, audible even through the television. Once it dissipated, the questioning resumed, but Ryland's lawyer seemed to be very agitated, tugging on his client's sleeve and speaking in a hissed whisper.

For the first time since the hearing had begun, Ryland looked discomfited, but that was nothing compared to his shock and horror when his own lawyer snatched a penknife from his briefcase and stabbed him in the stomach and chest.


Author's Note: To any Mitchell fans reading – Mitchell may have left SG-1, but he is not being banished from the story. He will continue to play a part in the series.