"Will it hurt?"

"Yes."

He felt the needle in the back of his head poking into his brain. He felt the connection disrupt inside him, his mind splint into pieces and he could still feel the Matrix trying to hold onto him. But suddenly it was cold, and there was pain, and he was trying to breath but he couldn't. There was a tube in his throat and he couldn't push it out. The world was red, and he was screaming with nothing coming out. Finally he broke to the top of the liquid and pulled the tube from out of his throat, where it scrape the insides, and for his first breathe, former Agent Brown threw up.

And the needle in the back of his head sent him messages and electronic shocks trying to get him to feel something that was not there, trying to tell his eyes he was in a room, trying to tell his hands he was feeling the wall, and his feet he was standing on the tile floor. But he wasn't, and all it did was give him a massive pain in the back of his head. He was cold, he was naked, and he opened his eyes for the first time, and saw the Real World.

"It will be overwhelming. Especially for you. You've never felt anything real in your entire lives."

Every part of him was in pain. But he couldn't stop seeing, he couldn't stop looking at was right in front of him. The World, the Real World, the endless bodies all trapped in that red liquid, all hooked up to the same machine, together as one entity. It was cold. It was so cold. His fingers trembled and he didn't know why, he wanted to look up, but he kept throwing up the liquid they had fed that body over it's life. He was coughing and breathing, gasping for breaths because he had never breathed before, and the lungs didn't know what to do, because it was overwhelming.

It was cold, and violent. The metal scraped the tips of the fingers and were cold on his palms, and the red liquid stuck to his body and made it colder, and he heard the machine rumble, and felt his toes and legs throb and twitch, but could feel his eyes were heavy, and his insides were twisted, and his throat, he couldn't breath, but the metal was scraping and it was cold, and he was seeing, seeing for the first time, and he didn't know, he didn't know it'd be like this, and he didn't know, he didn't know how to think about it anymore than he already was and the end was there but he had something to do and he couldn't forget but he knew forgetting was part of the process but he had something to do, something to do, something to do –

The War was over but the disposal of unscheduled humans who had left the Matrix was the same as it ever was. Release them, flush them, leave them to fend for themselves. The Machine grabbed Brown and did this as it had always done, as it had once done with Thomas A. Anderson. The pick in the back of his brain was pulled out and Brown swore he could feel blood pour out of the hole in the back of his head, and he thought for a moment in all his ignorance that the hole would allow the thoughts of the human brain to tumble out, and he was so afraid he was going to forget the one thing he could not forget. When this was over the liquid began to fall from under him and Brown was plunged down into what he remembered the Rebels called the Rabbit Hole. His mind was in a rush, his brain was sensing the world around him and firing up explosions in his head that was telling the mind what he was feeling, and he'd never, in his decades, centuries of life, had ever experienced anything even a fraction of what this was like. He was alive, he was real, with a real body in the real world, and it was unlike anything he'd ever known before.

"I came to you because I knew Smith trusted you. I trust you. I know you can do this."

It was too dark to see anything but he felt suddenly that he had fallen into water and with instinct he swam to the top and took in a breath. The body he was inhabiting had never walked on its own before, it was tired and aching already only minutes out of the Matrix. He was feeling weaker than he had ever felt before, his body was heavy, and he had trouble keeping his head above the water. Suddenly a name came to his mind.

"Jones?" He called into the dark.

Panic began to corrupt him, he realized he had no idea where he was, and for all he knew, in that darkness he could have been alone. And he kept thinking in his head the things he could not forget, but panic was taking over, and all he could say is Jones' name.

"Jones!" He called again. "Jones!" The water came over his face and into his mouth. "Jones!?"

A few days ago they were in the Matrix, Exiled Programs running from place to place with Agents constantly behind them. The War was over but not for them, Neo never told the Machines that Exiles had to be kept safe, and so the machines kept turning, and Exiles were still hunted. A few days ago they were living on their own. A few days ago Smith showed up at their door. A few days ago Smith made sure the Agents would never chase them again.

A year ago Smith had died and the War between Man and Machine had ended. A year ago they woke up in the middle of the street, miles apart from each other, and the next morning when the sun was rising they found each other. They hadn't been apart in all that time. They had chosen Exile when Smith left them and their Upgrades came, they chose Exile to find Smith. And when they did they saw he was a changed man, so to speak. He was not himself; he had become stronger, crueler even. Or maybe not, maybe he had always been that way; he was just able to express himself finally. He told them that he was going to conquer the world, and they followed him for as long as they could. They maintained their old ways as long as they could, desperate to create an illusion for themselves that they were the way they always were. Like they were still Agents, like they were never exiled. They followed Smith, blindly, they followed him for as long as they could, until the illusion broke and even they were assimilated into the Virus that was their leader.

On their own, they could not pretend anymore. On their own they were Exiles, and they were leaderless. On their own they learned to run, they learned to fight, they learned how to survive. And on their own they learned how to be humane. They never innately hated people as Smith did, they never felt anything towards people, they killed them because they were made to kill them, but they had no opinions of their own about people. And so, on their own, bit by bit they learned how to laugh, how to be angry, how to forgive, how to love. They made jokes, they had fights, they talked it over, they loved each other. They learned to live.

Then Smith shows up at their door, their makeshift home for the night. He looked like nothing had happened in that year. But he was once again different, for when they opened the door and stared at him, he smiled at them. He didn't have his sunglasses on and neither of them really knew how blue his eyes were. And he smiled at them, and asked if he could come in.

"I have missed you." Smith told them. "Both of you. I have missed both of you so much."

He seemed like a ghost, walking but not walking, so smoothly gliding over the floor. He seemed alien to the world, as if he wasn't really seeing everything that was there. He looked at their cups on the table as if he had never seen such things before.

"I have missed both of you. Excuse me, I'm still adjusting. I was scattered all over, the process was much more difficult than I anticipated. Forgive me. I have missed you both."

They didn't want to go near him, so he continued, gliding across the floor, looking at the smallest things as if they were all new to him. They were afraid of him.

"You're not Smith." Jones said abruptly.

"Jones." Brown tried to hush him.

"You can't be Smith. Smith is dead." Jones continued.

"Oh, Jones." Smith smiled, as if remembering some old and forgotten memory. "I always loved that about you. I have missed you so much. Brown, where's your tie? Oh, my, I'm sorry, I'm not myself quite yet, this is still new to me. I thought it'd be something like this, but I guess I wasn't so sure. Please don't be afraid, I'm just adjusting still."

"Your words are meaningless, who are you?" Jones pressed on.

Smith looked up and smiled. He went to the window and opened it, looking out towards the cityscape just outside the glass.

"I had to die to finish what I started. What we started."

Smith looked back at Jones and Brown, then he crawled out the four-story window. They gasped before running over to the window where they saw Smith sitting cross-legged on the mid-air, looking back at them.

"You are right." He said. "I am not Smith, but I am Smith. Do you see now?"

He was frozen in the air, flying without flying. He stood suddenly, on the air, and leaned into the window to meet their gazes.

"I am sorry, my behavior must be strange, I am still adjusting."

"Jones, be gentle with him." Brown told him. "He is obviously damaged in some way."

"Yes, thank you, Brown, you were always kind to me, always understanding. I knew you'd say that. I know everything you're going to say." Smith told him.

"Brown…"

"Smith, please, come back inside from the window."

Brown backed away from the window and held out his hand for Smith to take.

"I am Smith, I am not Smith." Smith said.

"Please, you must come inside now." Brown urged. "Someone may see you."

"That doesn't matter." Smith said.

"Agents will come." Brown explained.

"I'm hoping they do." Smith smiled.

Jones and Brown looked at each other.

"Smith. Please. Come inside." Brown said.

"All right, I will, because you asked so nicely."

Smith took Brown's hand and came back inside, but he didn't step directly on the floor, but rather hovered in the air within the apartment. Brown tugged on Smith's arm and led him to the couch where Smith sat, cross-legged once again.

"This is not right." Jones said. "This is dangerous."

"Jones, it's Smith, please…"

"It's not Smith, it said so itself. Brown, Smith is dead."

"I had to die to come back." Smith looked up at Jones. "It's so good to see you two. My friends."

"Smith, you're not making sense." Brown said. "Please, calm down, stop hovering, sit down on the couch like a normal person. Just, take a moment, tell us how you got here."

"How I got here?"

"Yes."

"I knew you were here, so I walked here. I mean, I didn't walk exactly, I don't have to walk because this place isn't real. Once you know that, I mean really, once you really know this isn't real, the rules are so much easier to break."

"Smith." Brown stopped him. "Stop it, be clear. Where were you before you came here?"

"At the Merovingian's Chateau."

Brown and Jones looked at each other.

"I'm sorry, I'm still adjusting, I can hardly see you, you know." Smith said. "I was in the Chateau, and I was coming to rescue Smith."

"You were rescuing Smith?"

"Neo was."

"Who are you?"

"I am Neo. I am not Neo."

Jones looked at Brown and motioned for him to follow. Jones walked over towards the kitchen, Brown looked back at Smith.

"Wait here, all right?" Smith nodded, and Brown followed Jones.

They stared at each other for a few moments, reading each other, already knowing each other well enough to know what would be said. Jones shook his head, but Brown leaned closer to him.

"He's hurt, Jones."

"No, I refuse to believe that's really Smith."

"But what if it is?"

"Brown. What if it is? What if it is Smith? Then what? What will he do? What will he make us do?"

"What are you talking about?"

"Do you want to go back to the way it was? Do you want to…just follow him again?"

"He's not fit to lead us anywhere, Jones, listen to him, something's wrong with him."

"What are we supposed to do?"

"Jones! Listen to him, he's hurt, and he came to us! He came to us. He wants us, he needs us."

"But last time we saw him, Brown, he killed us. It can't be Smith. It can't be."

There was a knock at the door; Smith got up to get it. Before Brown and Jones could tell him not to, Smith had opened it and there stood Agents Johnson, Thompson, and Jackson. Smith smiled at them.

"Good, I was hopi…" Johnson punched him in the face.

Smith fell back but his fall slowed and completely stopped before he ever hit the floor. He flew back up onto his feet with a smile.

"Please, come in." He flew back a ways into the room.

"Smith!" Brown yelled.

Johnson took out his gun and shot his entire round because somehow he knew his life depended on killing whatever was before him. But the bullets slowed and completely stopped before ever hitting Smith. They were frozen in the air in front of Smith, who smiled at the Agents.

"Don't move, Brown." Smith said, in a familiar and powerful way. "I have everything under control."

The Agents looked on towards Smith who merely smiled a now much more cruel and sinister smile at them. But the Agents, hooked up into the Mainframe of the Matrix could see the coding, and they could feel a disruption in the Matrix that originated in Smith, and they could see the coding that made him up.

"You are not Former Agent Smith." Johnson spoke up first.

"No. I suppose not anymore." Smith said. "Excuse me, I'm still adjusting." Smith landed gently on the floor. "Do you know exactly what happened to me when I first encountered Thomas A. Anderson? I mean, when I killed him?"

The Agents do not run, because Agents do not run, even as he comes closer to them.

"Thomas A. Anderson entered my coding and corrupted it. He…left a bit himself inside me, unknowingly. It was that event that caused the end of the war to occur. You see, he had disconnected me from the Mainframe, and made me no longer compatible with my programming, with my purpose. I could no longer be an Agent, I could no longer have a purpose."

He stops in front of them then, smiling at them.

"Now, due to their loyalty, Jones and Brown chose Exile with me. And thus, you, "upgrades" were created to take our place. And you did a fine job. You. Were wonderful. You hunted me, you killed me, you became me."

He breaks and laughs a little to himself.

"I want to thank you, for your hard work."

He grabs Johnson by his neck then his fingers dig into Johnson's very coding, he slams his fist into Thompson's chest, breaking his coding, and he kicks Jackson in the side. In one kick he takes Jackson's coding and parts it with his human host. He tears Johnson out of his host by the neck, and tears Thompson out by the chest. The human hosts fall to the ground, left unconscious. The three Former Agents scramble to their feet, realizing suddenly that they cannot contact the Mainframe.

"I give you, freedom."

They stare up at Smith, still trying and failing to contact the Mainframe. The horrible truth begins to dawn on them, but they deny it, they are Agents, they are part of the Mainframe, they are Agents, they are part of the Mainframe.

Brown couldn't stop from smiling. Jones looked down at him.

"Brown?"

"It must be Smith. No one else is that cruel."

Smith turned back to Brown and Jones; he began to hover the bullets upward. They came to him and began to spiral around him. Smith turned towards Johnson and the others.

"I suggest you start running." Smith told them

He held up an index finger where a single bullet began to spin, then he pointed, and the bullet fired, grazing Johnson's shoulder. Blood showed through his suit, then the Former Agents ran out the door.

Smith straightened his suit once they were gone; he wiped off some dust and looked up at Jones and Brown.

"I came here because I needed you to do something for me." Smith explained. "I am Smith, I am not Smith. I am Neo, I am not Neo."

Brown swallowed water and tried to stay above the water. He remembered thinking how happy he was to see Smith in his doorway. How happy he was to see that they were all together again. He had hoped in those brief moments that Smith had given up on his hate, that he had come to them because he had nowhere else to go. They'd be this sort of family again. They'd be able to live and survive together. But the thing that stepped into their doorway wasn't Smith.

"Jones!?" Brown called into the dark.

"Brown?"

Brown moved through the water towards the voice. His eyes were adjusting and he was already amazed at what he was able to see in the dark. They were in a huge waste room; old malnourished red liquid came here, pieces of machine debris, dysfunctional machine parts.

"Brown…?"

Jones called again, and Brown began to swim towards the voice. He hit a piece of some debris sticking up out of the liquid; he blindly waved his arms around until he finally felt the soft flesh of a body never before touched. The body moved and grabbed Brown's arm, pulling him down closer.

"Jones, are you all right?"

Brown felt the body, which lay sprawled out over the mechanical debris. Brown already felt that Jones wasn't moving like him, energized, and in a panic, this alarmed him, especially when Jones wouldn't answer immediately. Brown felt his head and he lifted it, feeling a warm liquid all over the back of his head. Jones was limp, but slowly grabbed onto Brown who now held his head up.

"I hit my head." Jones explained. "I didn't know it'd feel like this."

"Smith told us."

"I can't feel it, I can't hear you. What's going on? Where are we?"

"Smith told us it'd be like this. We'd have difficulty remembering why we're here. It's okay, Jones. Everything's going to be all right."

"I don't understand. Where are we?"

"We're in the Real World, Jones."

"Brown, I can't see you. How did we get here?"

"Smith, Jones, Smith came to us, remember? We have a mission, Jones, like the old days. We're on a mission."

They were in their living room when Smith, or whatever it was asked them for their help. They were home and the war was over when Smith or whatever it was came to them and told them the war was only beginning. They took a walk into the park where Smith said he'd be able to think better, and out there in the fake grass and the fake trees he seemed so at peace it was utterly unsettling. It's there in the park where a bench read "In Memory of Thomas A. Anderson," that Smith or whatever it was told them what must be done.

"I am the result of the merging of the Positive and the Negative. I am neither Neo or Smith, but I am both. I am The One, the true One. They combined their coding and their minds and their souls to make me."

When they asked why Smith or The One just looked at them with this peaceful expression.

"Because their work was not done, the world was not truly saved, because there's so much left undone. And they could not do it as separate beings. I am sorry, I'm still adjusting, still getting used to being me."

Smith walked behind a tree and came out looking like Neo. The human face smiled at them with such glee, and walked back around the tree and took on Smith's appearance, still with a slight smile.

"Everything is going to be okay now." The One said. "The world is dying, we left it dying, but we've returned to save it."

When they asked him to explain he only shook his head.

"It's difficult to understand without having the eyes of God. But…the ties between man and machine are so fragile, I know, I know I have seen it, this peace will fail, unless we do something. I am here to save man and machine, I am the Messiah of both species."

They didn't know if they could trust him, but he only nodded.

"If you're not Smith, how can we trust you?" Jones asked.

"But I am Smith. Everything Smith was capable of, I am capable of. I came to you because Smith would have come to you."

"What do you want us to do?" Brown asked.

He led them to the nearby hospital, a large and immense building full of the newly born and newly dead. It's there he spoke to a nurse, explained to her that they were visiting their brother, and she led them to this brother's room. It was a man in his early thirties perhaps, brain dead and in a coma, as he had been for the passed ten years. Smith touched the face of this man gently.

"Andrew Rainey, son of Cheryl and Robert, he was in a car accident and survived for a month before lapsing into a coma where he still is today. His mind has moved on you see, it's left the body, but the family has kept it here, perfectly intact." The One said.

"What do you want us to do?" Jones pressed.

"Go into the Real World and go to Machine City and find Neo's body. Connect it to the Matrix." The One said.

"What?" Jones asked.

"The Machines have lied to humanity, they have not recycled Neo's body, but merely kept it alive deep in the city, much like Mr. Rainey here. The body still shows signs of housing the Source and the Machines fear what will happen if they allow it to die. So they've kept it. I need you to go into the Real World and reconnect the body into the Matrix so that I may return to it."

"And how to you expect us to do that?"

"I will place you in bodies, all in the same farming facility. You will both be recycled. You will find each other and if you wait, a machine will come to find you."

"A machine?"

"He lives on an outpost by the ocean, he's been there for years ever since he was freed by humans. He will see you and he will find you and help you. Tell him what I have told you and he will take you to Machine City."

"…How do you know this?"

"Because I have seen it. I have heard it. I have lived it. It is difficult to explain. This has all already happened, Jones, it's constantly already happening."

Brown had taken a seat when they first entered the room. He was staring at the man on the bed, an empty body to be taken over. Just like when they were Agents, taking over people to carry out the mission. That's what this was, that's all this was, it was a mission.

"What makes you think we'll do this for you?" Jones asked.

"Because you are my friends." Smith said, The One said.

"Jones." Brown spoke up. "Let's do it."

"Brown, I think we should wait and consider our options."

"I'm sorry, but you won't have much time for that." Smith explained. "We must hurry. Tomorrow the Architect is going to die."

"How do you know that?"

"Because I'm going to kill him."

Smith took the time to explain to them what it was like as a program entering the Real World for the first time, as he had experienced with the human called Bane. Smith went into great detail the first few hours, which he said were going to be the worst. He told them that their memory would fail them and they'd easily get confused and disorientated. He told them their bodies were going to be weak and heavy and it will hurt to even move their fingers. He told them that it would take them days to work up the strength to even walk ten feet, let alone into Machine City. He said the food there tastes awful and the feeling of it in the stomach is terrifying and uncomfortable. He told them what fatigue and sleep was like. He told them what hunger and wounds were like. He told them how cold the Real World was.

He told them that he was sure they could do it, he told them Smith always thought they were stronger than him in that way.

Jones didn't want to. Jones refused. But Brown looked at him and told him they had a duty. They had a duty to Smith.

"Brown, he killed us, don't you remember?"

"Of course I do. But we knew he was going to, Jones. We knew there wasn't going to be room in his world for us. Eventually he would kill us." Brown told him. "But we followed him anyway, we helped him anyway."

"Why?" Smith suddenly asked in an innocent and curious way. "If you knew, why did you do it?"

"Because we believed in Smith. We believed in his world." Brown explained. "Remember?"

Jones looked at him, nodding.

Brown was holding Jones' head up, trying desperately to stop it from bleeding. He was holding onto the memory of Smith in that hospital telling them the machine. He was holding onto that image so desperately because he could feel it sleeping out of him already, panic taking over and not allowing him to think straight. He kept seeing that image in his head, and looking down at the body below him and telling himself it was Jones.

Jones' hand crept up to touch Brown's face.

"We're supposed to be fixing something, aren't we?" Jones asked.

"Yes. Everything's all right, Jones. We're going to be okay."

"I thought…I heard something."

Suddenly a noise came from above, a door was opening allowing in the light from above. A small, slightly humanoid machine looked down at them, two big green lights for eyes, looking down at them from a long neck.

"Do not worry." The machine called down to them in a voice that sounded like it was coming from an old radio. "I shall get you out there!"

Brown looked up at Smith, or whatever it was.

"Do you mind if we still call you Smith?" He asked.

"No, not at all. I'd prefer it if you did." Smith, The One explained.

"Will it hurt?"

"Yes."

-------

I hope everyone's seen "Matriculated" from the "Animatrix." That's going to become important.