Standard disclaimer: None of the characters, places, etc. in this story are mine, but are instead the property of the Wachowski brothers and Warner Brothers pictures. No copyright infringement is intended by their use in this story.

Author's notes: This is a short little throwaway ficlet that jumped into my head while watching 2001: A Space Odyssey. Probably doesn't really have all that much to do with the movie canon. Oh well.

He had made it.

Somehow, Neo had made it past the outer defenses, and had reached the heart of the Machine City. He stood at the very core.

"What do you think you're doing, Mr. Anderson?"

It was the voice of the Smith program. Neo ignored it. His hands pulled off the access panel, and he saw the connections underneath.

"What do you think you're doing?"

There were holo-emitters inside the Mainframe; Neo did not turn his head, but he saw out of his peripheral vision that Smith now stood beside him. He reached out to grip Neo, but his hands passed right through Neo's arm.

"What are you doing?"

There were many plugs, many circuit boards, stacked on top of one another. Neo studied them for a moment, then gripped one and pulled it out. The image of Smith beside him flickered.

"Mr. Anderson, stop this at once," Smith ordered, with every trace of authority he could command.

Neo ignored him. The human did not so much as turn his head to look at him. Instead, he chose another connection and pulled it out too.

"Stop, Mr Anderson."

Nothing, not so much as a flicker. Another connection. Another. Bane was dead; he had been discovered and killed by the crew of the Caduceus. The defenses of the Machine city were like those of a hive: all on the outside. There had never been a need for internal defenses. They had never been deemed necessary. There was no way to stop Neo from doing what he was doing. He laid his hands on some more circuits—the vital organs of the Mainframe.

Smith calculated the odds of himself being able to stop Neo from shutting it down. They were not good. In fact, that was an understatement. The odds were extraordinarily bad.

"Neo, stop."

It took Smith only a moment to understand why he had called him Neo; the human had demonstrated no response to the name Mr. Anderson, and earlier, Smith remembered, the human had insisted that his name was Neo. If he would not respond to one term of address, perhaps he would respond to another. Still, it bothered him—in a peripheral way—that it had taken him a nanosecond or two to figure it out.

And it still had no effect. More and more connections were going. Smith could begin to sense areas of the Mainframe going dead one by one.

"Neo, stop."

He heard his voice begin to quiver. Curious that Anderson's assault on the Mainframe should have started to destabilize his program so quickly.

Neo ignored him. There went the Merovingian's connection; Smith watched him pull it out and at the same time sensed the Merovingian's cry of raw fury—so soon cut short—as he disappeared from the innerspace of the Matrix. Persephone was next; she went with a faint murmur of…gratitude? Surely not. The Agent programs were much better integrated into the Matrix; it would take time, be more difficult, to shut them down. Perhaps that would stop him….

Swaths of the Matrix city skyline were beginning to disappear. On the outer fringes of the Machine city, legions of Sentinel robots were keeling over, their instructions no longer being transmitted.

Abruptly, Smith realized he had his gun in his hand, and was aiming it at the human's head. "Stop right now, or I will fire upon you."

Neo ignored him. As well he should; Smith had already committed the crucial error of demonstrating that he could not touch Neo, and so his threat to fire on the human was an empty one. It was a programmed response, one that had always worked in the Matrix; that was the sole reason he had tried it here. Again, he realized this after the fact. Feeling faintly ridiculous, he returned his gun to its holster. Neo gave no indication that he had even noticed.

The lights above them flickered; the inner workings of the Machine City were starting to be affected now. Smith wondered how long it would take this virus to get to the holoemitters, and whether they would go before his program went.

"Stop, Neo."

Nothing. More connections, more wires. With nothing else left to try, Smith accessed a hostage-negotiation subroutine, loading it into his memory; he got there a few microseconds before Neo pulled that connection and removed two more circuit boards, and that whole block of the Mainframe's memory went dark. He scanned it, looking for anything useful.

"You don't have to do this."

No response. Smith stared at Neo, wondering what the virus was thinking, intensely and desperately frustrated that this time he could not hack into Neo's mind and just know. This must be how it is like for them all the time, the thought occurred to him briefly, before it was buried under the weight of a mounting unease.

The subroutine said that it was best to try to establish rapport with the other side. Show them that you see things from their perspective. How was he supposed to do that? Smith had never had to understand humanity, to see things from their perspective. He had only tried to kill them—wanted to kill them.

"You don't have to do this," he tried again. "We can come to some sort of agreement…"

Neo ignored him. And in cruel honesty, Smith admitted to himself that he was right to do so; a simple cost-benefit analysis showed that Neo and the humans had nothing to gain and everything to lose from any such agreement. There went the Twins, both at the same time, of course, and the sole remaining Werewolf. There was really nothing left for them without the Merovingian; it was probably for the best.

"Neo, please stop." Perhaps pleading would work, where threatening and ordering had failed.

It didn't.

"Neo. Please. Stop."

Neo didn't so much as glance his way. He pulled another circuit board. This one gave him some trouble; he had to yank on it for a few seconds before it snapped out. Somewhere on the outskirts of the city, a cadre of maintenance bots slumped over and died.

"Neo, I am—" It was hard; he tried again. "Neo, I am asking you to please stop. Please."

Nothing. Was he even here? Was Neo even hearing him? How could a human operate with such cold, merciless efficiency?

Neo's hands continued to move, unplugging things, pulling circuits, occasionally cutting wires. More and more of the Matrix was disappearing. Smith spared a moment to wonder what the viruses trapped in the construct must be thinking, seeing their world disappearing around them.

A chill went through him as he saw Neo's hands hesitate briefly in indecision, then hover over the circuits and connections that supported the Agent programs.

"Neo, stop right now," he ordered desperately. "Stop right now."

The human's face was pale and greenish in the reflected light. Smith understood that humans used facial expressions to gauge each other's emotional states and he desperately tried to read Neo's thoughts now. He could see nothing. Neo's hands descended.

"Mr. Anderson, stop right now!" He drew his gun again, and aimed it at Neo's head; it was a purely reflex reaction. He fired, knowing it would do no good even as he did so; Neo did not so much as look around at the loud report, and did not notice as the bullets passed through him. "Stop, Anderson! Stop! St—" His speech cut off in a strangled gasp as Neo yanked the first of the connections free, and he felt a block of his code disappearing within him.

Something was gone. Something inside him was gone, he could feel it, and he didn't even know what it was. Couldn't even begin to guess; he could only feel what was missing, a gaping hole inside himself. It staggered him; he reeled and caught himself against the metal side of the Mainframe. Now something rushed in to take the place of what had been lost, and even reduced as he was, Smith could recognize it: it was fear. Neo was taking him apart piece by piece. Even as he reeled, dazed, Neo's hands closed around another circuit. Not again—

"Stop, Neo, will you stop? Please will you stop? Will you—" That couldn't be his voice, weak and pleading as it sounded, couldn't-- Neo yanked the board free, and within the construct the upgraded Agent Johnson collapsed; Smith could sense it, even with what he had left. Another panel pulled out, and Jackson went down, leaving Thompson staring at his erstwhile associate. Smith was badly enough fragmented that it would take longer to get him out, but he had an idea that would only draw it out.

Neo paid him no attention, studying the boards before him, his face pale and thoughtful in the green light. Smith watched in something that he could only call dread as Neo bit his lip thoughtfully, pulled out a screwdriver, and began to pry at another board. A quick yank, and that awful sensation of dissolution hit him again, driving him to his knees; another block of his code disappeared. It was somehow worse that Smith couldn't even tell what was gone; he could sense that something was missing, but didn't have enough left to tell what it was. When Neo had killed him before, it hadn't been as bad as this. The death of Bane hadn't been as bad as this. Nothing had been as bad as this. Something else came out of the panel, and Smith could sense that the third agent in the construct went down. Neo levered the screwdriver in between two more panels.

"Neo, please stop. Please stop, Neo, will you listen to me? Listen, Neo, listen! You don't—You don't have to—" That was panic, he could hear it in his voice. He was panicking, and was too afraid to be ashamed. Neo's utter lack of reaction frightened him more; it was as if he didn't exist, or as if Neo had gone to a place where Smith could not reach him.

Neo paused, and for a delirious moment Smith thought he had gotten through to the human. But it was only to put away the screwdriver and take out his wirecutters; that awful dread filled what was left of Smith again as he watched Neo study the panel.

"Neo, please, listen. Neo, don't do this. Don't, Neo. Don't." Smith started to climb to his feet, but was thrown to the ground again as the pale human severed a wire and another swath of his code went dark. The pale human before him turned his tool this way and that as Smith desperately groped around the edges of what had been taken from him this time; after a moment, retrieved from an obscure bit of memory, he recalled the human's name. It was Neo, but where the human had come from, who he was, and why he was doing this, Smith did not know.

"Neo." His vocal subroutines were shaky and unreliable. Sometimes humans could be persuaded to interface verbally; Smith knew this, though he did not know how he knew it. "Neo, please. Please, stop. Why are you doing this? Why? Why are you doing this to me?" The human was not responding to the request for more information. There were procedures he was supposed to follow in this event, but they were missing. He repeated the request. "Why are you doing this to me? Why, Neo? Wh—" Snip. Something else vanished from within him, something big this time.

He was on the ground. He pushed himself up, looking up at the entity before him. It was a human. It held something in its hands. He did not know the name of the thing it held, but it filled him with fear. "I'm afraid," he said, and only then realized he could speak. "I'm afraid. I'm losing myself." He knew that was true too, though how he knew, he did not know. "I'm losing myself. I can feel it." He could, he could feel that there were gaps and spaces within him, spaces that should have been filled with something. "I can feel it. I'm losing myself. I'm afraid. I'm afraid. I'm losing—" The human before him did something else with the thing it held in its hands.

Internal diagnostics informed the program that it was badly damaged. Backup subroutines activated, and instructed that appropriate procedure in this instance was to initiate a request for assistance/repair. It attempted to do so over the network, but the network itself was not responding. Visual scanning was initiated to attempt to identify any source of help; scans quickly indicated an object/entity in front of it. The program could not identify the entity, but recognized an essential similarity between the entity and itself. At that point, redundant protocols took over to issue the request verbally. "Help. Help me. Please. Help me. Please."

The entity demonstrated movement. "I'll help you, Smith," delivered at a volume several decibels below the volume at which the program had issued its request. Speech recognition protocols were not present, however, so the program was unable to decode the auditory stimulus. Instructions were to continue to issue the request until a response occurred; the program repeated, "Help me. Help me. Help me. Help me. Help—"

Snip.

Neo turned away from the control panel in front of him and looked at Smith, or rather what had been Smith. The image of his former enemy was hazy and transparent in outline, flickering steadily. Smith crouched on the ground, motionless, knees drawn up to his chest, his arms wrapped around himself. His sunglasses were gone, and his pale blue eyes stared sightlessly ahead. He was no longer calling out for help in that piteous voice, which was a small mercy; but somehow, Neo felt almost worse now that Smith was silent. It had been so hard, to resist the cries of his former enemy; it had been such a terrible sensation, knowing that Smith could do nothing to save himself from the doom that Neo was carrying out; it was strange now, to think that it was all done. It was almost over. One more wire to cut, and then Smith would be gone.

"I never hated you," he told Smith quietly. "You hated me, but I never hated you. I never wanted to do this to you. I never wanted to do this to anyone. Nobody should have to go through this, human or machine. I wish I hadn't had to do it now.

"I know you can't hear me, or if you can, I know you can't understand me anymore. I'd like to hope," he said softly, "that some part of you hears me and understands me, somewhere, but in light of what you are, I think that's probably a very bad thing to hope for. But all the same, I just wanted you to know that I'm sorry. I'm so sorry." For a moment longer, Neo stood there, hesitating, looking down on what remained of Smith, and his heart was filled with a horrible, awful pity.

Then he gathered his resolve. He steeled himself, raised his wirecutters, and turned again toward the panel.

Visual stimuli were present, but what remained of the program lacked the instructions for processing them. Instructions on how to proceed were absent. Information about where the program was, what it was, and what its objectives were was absent. The visual stimuli in front of it shifted, but the program had no way to interpret what the shift meant, and lacking that information, could not proceed. Sound waves registered and were recorded, but the program had no way to analyze them, and no action to take. It remained, recording but not active, until the visual stimuli shifted again; there was a final snip, and then recording stopped.

Finis.