A/N: I must have written about a thousand outlines for this thing, and I've still never bothered to finish it. *insert self-deprecating comments* At any rate, here are a few things worth noting:

1) This is set three months after the end of Revolutions, in an universe where Neo was resuscitated in 01, and Smith's programming wasn't quite erased. The movie ending was ambiguous(ish), but I'm going to call this one and say the Wachowskis killed them off for good, so in that sense this story is an AU. That said, I've tried to write it so that it could theoretically follow the trilogy with no explicit changes to canon. Anything inconsistent is a mistake on my part.

2) Someone mentioned Neo's eyesight in a review a while back, and yes, Neo can see. That will be explained eventually (I hope), but for the moment I'm working off the principle that if the machines can do something about the viscera-liquefying electric shock Neo recieved at the end of Revolutions, they can repair and/or replace human eyes. Whether they would is another question, since blindness is non-life-threatening, but I think they'd be a little unnerved by Neo's ability to see the Source without interference in the Real World, and would probably take the opportunity to rid him of it while still technically doing him a favor.

3) A lot happens over the course of the trilogy. Neo gets more confident/competent/responsible/etc, but he also, ironically, loses a lot of his ability to connect with the human race. I think Trinity represented the last of that for him, and while it's pretty obvious how intense his grief for her is, I feel like the repercussions of her death would extend much farther than that. I'm not trying to write him exactly the way I see him in the movies, as I don't think he really would be anymore. But again, I make mistakes, and if anything about the portrayal seems unrealistic or way out of character please say so. The same goes for Smith and the others. Comments are more than appreciated.

Initium, -i n: entrance, beginning

It's silent.

If they could be honest with themselves they'd say it's the silence that makes it intolerable. There are four men on deck and none speaking. Their movements are all tamped down. The engines are too loud with no one there drowning them out.

It goes like this: The captain is tired. The commander is sullen and they're clashing. The operator hasn't left the monitor in hours and the mechanic is hiding below deck. The lieutenant—and he'd never get used to the title—is standing a ways to the side, dreading the moment when the tension finds air to start burning. The place is pin-drop silent, he's thinking, and they can't afford this. If they aren't careful, the whole room will go up in flames.

*

It's been weeks since the message. Three and a half, to come down to specifics, and more than one person is counting. 01 was brief, and that was normal, no extra information, no addendums, just a transmission requesting immediate counsel. They asked for the One specifically—the Anomaly, as they would probably always call him—and that was not normal. They had ways of sounding urgent in only a few words. Asking for Neo was, undeniably, one of those ways. Demanding him 'immediately' was another. Zion responded immediately.

The Council sent Morpheus to accompany him, and the military sector sent Locke. Two days later, the three met the Machines' envoys out in the tunnels, at a neutral point between the cities. The location had been set for some time. It was not rare for them to use it. A good three months into the peace, this sort of negotiation could almost be considered routine. It was the tone that kept Zion off-kilter. The request for Neo and not an ambassador. There was talk of traps and betrayal amongst the public, but after one hundred years, the Council felt certain it could recognize hostility. 01's transmission did not feel like a threat against Zion or her people. It felt like a distress call.

If Neo read anything more into the message than they did, he never said so. And he himself could not be certain that he really knew. He berated himself for paranoia in those first few days. He was as surprised as anyone else when the other shoe came down on them, and no one could deny that. But, if pressed, he'd have had to admit he had guessed something well before all the commotion. The program called 'Smith' had not died, he was sure, and they were bound to hear from him eventually.

There were reasons for him to suspect it—the Oracle's words to him, for one thing, words like opposite, and negative, and balance. Her words were to be taken with a grain of salt, but he'd felt it too—that vague, amorphous sensation. Who was to say either one of them would ever really be gone for good? Neo himself had been resuscitated by the Machines only a few hours after the end, and even then he'd felt something, far from his mind as it had been at the time, shivering on a platform in the dark. He'd always been able to tell. And, guiltily, he'd have to say a part of him knew this was coming. He'd hoped it wouldn't. He'd hoped—maybe—that one day the feeling would take care of itself, that the neglect would make it disappear, and he'd never have to believe that it was real, or valid, or there. He'd just know, then, that Smith had been deleted and it was over. Maybe. He's not sure.

It never happened. The System, the envoys informed them, had been attempting to delete Smith for months. And failing. No one was quite sure what went wrong. They'd been keeping him in a separate construct, sealed off from the Matrix. It was impenetrable. They'd had perfect control. But even rewriting their purge program had earned them very little progress. It was possible, they said, that Smith's code had become so entangled with the system that deleting him now would be impossible. It would be like destroying a cockroach. And after four successive tries, no one's really willing to risk doubting that anymore. They've all been well-versed in the consequences of wasting too much time.

*

"But what do you need us for?"

The red eyes shifted to face him, two lights in a metal skull. He supposed it was meant to look human. The similarities never failed to unnerve him. "The Virus must be removed from the system at all costs."

Neo stared down at the tabletop, breaking the beginnings of eye contact, or something very much like it. The machine looked distressed—if it were possible for a machine to even feel something so basic and visceral.

"You are aware that it is possible to download a program's consciousness into the physical world?"

There was a pause long enough for Neo to confirm that before it went on.

"If deletion of the Virus is impossible within the system, it was thought that its destruction could be completed outside of the Matrix." Another pause. "But a droid in the physical world necessarily possesses a heightened connection to the Source."

Neo nodded, finishing the thought, "And that would be too dangerous."

"Precisely."

"But then what do you…?" He trailed off and the machine almost seemed to squirm. Is it nervous? Can they get nervous?

"The process has never been attempted with a human vessel…."

*

The body that is to be Smith's is strapped to the jack-in chair, restrained as much as they could manage, Morpheus and Locke on either side, waiting. They're all waiting.

Link is sitting at the monitors, conducting what may be the most complex hack of his life as he wades through encryption. The others are engaged in pointed silence. Neo is standing by the wall, watching, telling himself he's standing guard because they may need him before the end.

They are three days out of Zion. They'd taken one to reach broadcast depth, and another to set up the equipment. The crew was kept small—only the four of them on deck, and a novice mechanic along for ship maintenance. They have orders to stay out for three weeks before coming home, all the while holding Smith as their captive on board. In that time 01 will run scans through the system, assure themselves that bringing Smith into the Real World will serve its purpose. No one wants to see him come back, least of all after this. His execution is left in limbo until they know. They are exactly on schedule.

*

Neo could feel his mouth go dry. Yes, it had been attempted. Yes, it would work. Of course it would work.

It was partly his fault. He'd never made it public. When it really came down to it, no one in either city knew what had gone on once the Logos left the Hammer that last night. They had what was necessary, what they'd seen and been told of in fragments—the wreck of the ship, Trinity's death, Neo's bargain—the abrupt and violent end of a very long war. They knew the basics. They knew the end result.

But the specifics were something Neo had kept to himself. He'd been in no condition to explain when he first returned to Zion, and even later, when others pressed for information, he'd only say what they needed to know. That much was difficult enough. They didn't need the rest. No one knew exactly how the ship had reached the city or how it had crashed. No one knew the details of Trinity dying in the wreckage, how seriously they'd been attacked or that Neo had been blind.

And no one knew about Bane.

For all intents and purposes, Bane was a madman suffering from the effects of VDTs. He'd stowed away on the Logos, caused a brief struggle, and then it was over. That was all there was to say. Neo had not corrected the assumption. To give the rest would be to relive every moment that Smith had held a knife to Trinity's throat, to remember having his eyes cauterized by a metal coil, to remember the feeling of being unable to see the woman he loved in the last few seconds she was alive. He recounted it to no one. At times he felt he should have explained—at least for the sake of clearing Bane's name—but he never told them. And, after a while, no one asked.

And now, once again, it was back to being real, an unpleasant fact and not a bad dream born of post-traumatic stress and long nights, and Neo debated for a moment whether he needed to say it. Whether he could even open his mouth. The room was waiting for his answer and he couldn't seem to break the silence.

He was spared the effort. "Bring that thing here? Onto one of our ships? Are you insane?" The two envoys turned to see Locke, clenching the edge of the table and glaring.

"We see no other alternative."

"No." Neo's own voice was hoarse, barely audible. "You can't do that."

*

He didn't tell them, didn't mention Bane. Even then, he wasn't willing to touch that last resort. But he did as best he could to persuade them without it. It wasn't about the danger. In spite of everyone's gut reaction, the ordeal wouldn't pose much of a threat. It would last twenty-one days—thirty at most—during which time Smith would be kept in a cell, under lock and key, in a ship a good twenty miles from Zion, and with no more physical power than a human shell could offer him, there was only so much he could do from a cell. Once the Machines had finished scanning the Matrix and were satisfied that he was no longer there, the crew would execute him in the Real World, and that would be the end of it. Twenty-one days was five hundred hours, was thirty thousand minutes, was two million seconds. It would be quick. No one would be hurt.

But what they were planning had crossed the line from execution into something like murder. Killing in the Matrix had been one thing. It was necessary. One had to adapt. They'd been at war. And Neo had seen Smith die before. They were both damned, it seemed, to a series of trivial deaths at each others' hands. He'd killed him again—and again—and it had all mattered so little so long as the war could be brought to an end, so long as the human race could go on living. It has a different cast to it in peacetime. This will be so much longer, so much more drawn out and humiliating. The urgency is gone. He doesn't feel right without it.

Smith hated him. Neo was always aware of that. But it was a sentiment he'd never quite managed to return. He'd disliked him, wished him dead for all the right reasons. He'd been angry with him, and—far enough back—a little afraid of him, but that doesn't amount to hatred. Hate takes energy, devotion, and there had been more important things during the war. There had been Zion and the prophecy. There had been Trinity. Smith had never been the only enemy. His death was not the goal. And Neo had felt very little towards him. It was only there, in that room, that he'd found himself wishing he had some hatred to justify what they'd do—he'd wanted so badly to argue. By the end of the meeting he was grasping at straws.

He reminded himself who this was—what this was—and it was easier. He closed his eyes when the decision was made. There would always be choices like these. He would never get used to them.

*

"You don't want to do this either."

"For the sake of the treaty, it must be done." Morpheus's tone was off as he spoke, straining with forced assurance and calm. Neo watched him from across the room, shot him a look that said 'I know you don't believe that' and kept silent. Morpheus was pacing. Neo was leaning against the far wall with his head down, staring at the floor. They were alone. Time passed and no one spoke.

After ten minutes of nothing, Morpheus stopped at the door and turned. "The ship leaves tomorrow."

*

"Alright, sir, I think I got it. But this is gonna be messy." Link shoots a glance back at the captain and he nods.

"Go ahead, Link." And there is the strain, again, in his voice. Neo wonders if he was the only one to notice, if Morpheus even noticed himself. Link's keystrokes slow down as he approaches the end of the sequence. Neo follows the code for a moment with his eyes. Five seconds to go. The others are watching it too. Every five minutes for the past half hour, someone's looked back at that screen. Link hesitates a moment and hits another key, turning back towards the deck with a tense little smile. Another moment passes.

"Here we go."