A/N

This would have to be one of the most difficult oneshots I've ever done, having started it sometime in April and added to it piece by piece until recently. Even now, I'm not completely comfortable with the result, but I still feel that it's at least passable.

In terms of timeframe, it takes place during the movie, shortly after the second arrival at Haven, only to see the Alliance's handiwork. I'm stretching the actions involved here in regards to canon, but it's meerly for the sake of execution as opposed to being AU.

Choice

Simon Tam had never been one for misbehaving.

Well, that wasn't entirely true. "Never" was just that-never. And unless he excluded the last eight months of his life, the statement no longer held any truth to it. After all, one did not exactly fall on the right side of the law when they fell in with a bunch of criminals whose respect for the law ran no deeper than the water of a cesspool. And although it could easily be argued that it had been the law who had driven him off over the line it had drawn and spat on him as he did so, he could still remember a time where he would have made an effort to get back on the right side of it.

Times change though, he reminded himself, making his way up to Serenity's bridge. Sometimes subtlety, sometimes…sometimes…

He shook his head. Nothing was to be gained from reflecting on a life that was beyond his reach, not to mention one that he wasn't even sure if he even wanted to go back to. For better or worse, he'd become used to his circumstances, ranging from the ship which provided transport to variations in said circumstances to those who dwelt on the ship itself. It had been like that from day one of the rest of his life and would either continue to be so or lead to a final change of circumstances in incarceration. Or death, if one could even see a difference between the two.

Death and circumstances were linked on Haven it seemed and the Alliance seemed had proven itself perfectly adept at dictating the terms of both. As the dominant force in the 'Verse, it was undoubtedly in a position to do so. But Simon doubted whether, even in its realm of knowledge and power, fully understood the concept of cause and effect. That its actions had led the captain to making a shot at Miranda, that the Alliance's own actions may, just may have provided the catalyst for its fall from grace.

Sitting down by the comms. console, Simon knew that even in these circumstances, the captain could appreciate the irony present in an otherwise grim situation. But even if he was able to do so, the surgeon doubted that it would sway his wrath at what he was doing. Being pushed down on the dining table was bad enough and even after all this time of being part (or "associated" as Jayne often pointed out), the good doctor still remembered the original threat of being dumped out the airlock he'd received after Dobson had revealed himself to be both an Alliance spy, albeit one who couldn't shoot properly.

I'm not a good doctor, he thought bitterly as he re-established the uplink of the video feed. If I was, I wouldn't still be on this ship. And I certainly wouldn't be-…

The screen flickered on.

…consulting with an operative.

Simon knew of operatives. One didn't consort with people ranging from "undesirables" to "dangerous terrorists" without picking up a few facts about the government whose actions you were opposed to in regards to your seventeen year old sister. Yet all the tibits of information he'd come across in his two years of illegal activity hadn't prepared him for a face to face confrontation. A confrontation with a monster. A confrontation with the murderer of innocents. A confrontation with a man who, uniform aside, looked so…normal.

Normalality was generally anathema to Serenity and its crew.

"Simon Tam…" he said slowly. "I will admit that I am surprised."

"You're not the only one," the doctor answered solemnly, almost as if he was judging himself.

"Have you seen reason then?"

"Reason?" he laughed. "Yes, seeing mass murder has really enlightened me to the-…"

"Sarcasm isn't your strong point doctor, and considering that Captain Reynolds was talking to me only a few minutes ago, ending the conversation in most un-agreeable manner, I'm guessing that the time you have available for this transmission is limited. So I therefore suggest that you get to the point."

The doctor blinked. He was used to being talked down to of course. That's what happened when you were at the bottom of the hierarchy that Reynolds had set up (himself at the top, the crew in the middle and Simon and River at the bottom). But for someone from outside that hierarchy to do it, from someone who hailed from a society where he'd once been counted amongst the best and brightest…it was an alien feeling.

"I assume that you're here on the subject of your sister," the Operative continued, pressing his advantage as he laid back in his seat-a typical sign that one has the upper-hand in a conversation.

"You could say that," Simon answered, replicating the Operative's movements to convey his own sense of authority, even if both of them knew that it didn't exist. "She's been-…"

"The source of much travel for you, your friends, and mass murder," the Operative interrupted, suddenly leaning forward. "Which brings me to the question I have to ask you. Why protect her?"

Simon blinked, the question having caught him off guard. He'd always wondered how he was going to protect River of course, especially when the subject of harboring fugitives was brought up on Serenity, but he'd never asked himself why. Nor had anyone else for that matter.

"She's my sister," said the doctor eventually.

"Which means what?" the Operative asked.

Simon raised an eyebrow, not comprehending. What other reason was there?

"Dr Tam, despite the Alliance's efforts, there are thousands of people scattered throughout the 'verse who are in even worse shape than your sister. Physical, mental, and sometimes both. You treated them back on Osiris, but I doubt that you'd ever lay down your life for them." The Operative leant forward, clasping his hands together as if he was praying for the salvation of Simon's soul. "Which therefore begs the question of why you should give your sister preferential treatment, especially considering the…extreme circumstances."

Simon couldn't help but smile at the hesitance behind the Operative's use of the words "extreme circumstances", especially considering that it was the Operative himself who had set them in motion. The only question was whether he actually felt any remorse for the slaughter on Haven or was simply a poor actor at conveying it.

The Operative's other words were a bit more disturbing however, especially since he didn't have an answer for them…

"I'll tell you why you do it," said the Operative, as if reading the fugitive's mind. "You do it because instinct drives you to do it."

"What!?" Simon spluttered. He'd been complimented on rationality and calm thinking before, but never instinct. That was more the realm of Reynolds and Jayne. A realm that Simon didn't particularly feel like straying into.

"Altruism is merely a response to natural selection, something that was developed eons ago back on Earth-That-Was," said the Operative, his tone and the look in his eyes suggesting that he was merely repeating information that had been driven into him. "However, we've left behind our homeworld, left behind our old barbarities. There's no need to follow old instincts."

Simon nodded. "I see…and slaughtering innocent people isn't barbaric?"

"Merely the result of a bunch of naive fools following instinct rather than rationality, emotion rather than logic, their hearts rather than their…"

Simon drowned the Operative's voice out, his mind racing. He'd seen the ugly side of the Alliance-most of Serenity's crew had. But even after all his experiences, he'd never understood exactly why the Independents had fought as long and hard as they did during the Unification War, fighting what was a lost battle from the outset. Now however, he was beginning to understand. Instinct had driven them to do it, just as rationality had driven the Alliance to seek to expand its control. Those of the 'verse had had to make a choice during that war. Just like he had to make a choice now…

"So what will it be doctor?" asked the Operative, having finished his tirade. "What side of you will you follow?"

Simon sighed. Sometimes he wondered why he did it, why he abandoned his old life on Osiris, why he continued to put Serenity's crew in danger, why he continued to look after a psychic assassin who if recent events were anything to go by, wasn't set to become akin to a normal human being in his lifetime. Yet whenever he wondered about this, he also wondered how he'd live with himself if he did follow that path.

Simon smiled. Serenity hadn't changed him. It had merely awakened instinct that had been there all along, just cast to one side as "civilized" life demanded it. He always had a choice…

…and like the Independents before him, he made it.