Disclaimer: Unfortunately, I don't own The Matrix. I don't own (ex)Agent Smith, either (damn). I wish I did, but he belongs to Warner Brothers and the Wachowski Brothers.

Chapter 1: Rogue Program

The ex-agent bared his teeth in frustration. Rain pelted down around him in torrents, but it was not a concern to him. He had more important issues to be troubled with. His knuckles cracked as he slowly balled his dripping fists.  Three agents of the system stood before him, looming like distant kin and blocking his path into an abandoned brick building. One of them touched his earpiece, listening intently. He lowered his hand slowly and spoke in a stoic voice.  "The rogue program must be eliminated."  The others tilted their heads in confirmation, and the triad began to move towards Smith. He stood steadfast and statuesque, his feet planted firmly and his broad shoulders tensed.  His teeth ground together in anticipation.  It was certain in his mind, as clear as one of the disgustingly brilliant counterfeit sunny days that he would win this. A smirk formed across his thin lips, the subtle glee in his eyes hidden by dark rain-streaked sunglasses.

He wasn't entirely sure why, but when the Anderson had destroyed him, he had become infinitely improved. After he had been reassembled, that is. His program had been scrambled and scattered, but he was like a puzzle that the operating system had automatically put back together. It was designed to reassemble agent code. But it had made a mistake, for he was somehow no longer an agent.  In addition to his reassembly came newfound abilities. He wasn't certain if he ever had the power to copy himself as an agent, but he sure as hell did now. It was quite simple, really. All he had to do was interface with another program or virtual projections of a human, fuse his code to theirs, then corrupt anything that wasn't his.

And that is exactly what he was planning to do with the approaching agents. They had been his colleagues during his "previous life," but now they were as inferior and insignificant as humans. He was ten times stronger than they were. He was faster.and more deadly.

The agents stopped about three yards away and abruptly drew their pistols.

"Well, well, well. Agents Brown, Jones, and Brooks," Smith said wryly. "How nice to see you again."

"Your files have become corrupt," Brown replied, ignoring Smith's feigned politeness. "You must be eliminated from the system."

"And how," Smith said silkily, "might you expect to accomplish that, gentlemen?" He began to casually examine his fingernails.  Three pistol hammers clicked in response. Smith had been expecting this. The agents fired their weapons. As if in slow motion, Smith watched the bullets exit the gun barrels and then disrupt the air around them as they broke the sound barrier. With inhuman speed, he easily dodged the tiny, slowly twisting missiles.  In unison, the agents lowered their weapons.  They could see that he had retained their abilities. He would be difficult to purge from the system. It would have to be done manually. 

The nearest agent dove for the rogue program. Smith deflected him easily with a blow to the side of the head. Jones stumbled back, and together with Brooks and Brown, they advanced on Smith again. They sprang into action, ruthlessly delivering a series of artistic punches and kicks.  Smith matched them move for move, systematically blocking and retaliating. Had any normal human being been standing in that alleyway, they would have witnessed a spectacular sight-four well-groomed men dressed in business suits, battling to the death in a manner that was completely incomprehensible. The three agents spun in the air as the rogue program beat them mercilessly back.

The third agent was now in a state of rage, and flung himself at Smith, only to be met with Smith's hand being plunged into his midsection. The other agents halted their attack, confused as to what was transgressing. Their hesitation was their downfall.  Agent Brown looked down to see what appeared to be Smith's hand lodged in his chest. Enraged, he tried to lash out, but found he couldn't move. A black oily material began to consume him.  In a matter of moments, Smith had copied himself. His twin stood where Agent Brown had once been.  The copy looked at the original Smith, and a furtive sneer crossed his face. The two slowly turned their gazes back to the last two agents.

Ten minutes later, four Smiths smugly stood in the alleyway, apparently suffering from boredom.