The machines clinked away at their circuitry. Zapping green slabs of silicon, sending sparks flying in every direction. The machines had been working constantly for the past year to develop the new Matrix. Now that they had Neo, everything was running smoothly. The Power Plant had been finished and was ready for the first human inhabitants. The machines slowed their pace and then altogether stopped.

"It is finished," said the unified voice of the machines.

The machines stood up and began to assemble the silicon pieces into a massive motherboard that would become the mainframe for the Matrix. The dark room the machines were in was a large sphere with copper wiring running throughout the interior. Everything within the Matrix system was connected through this system and routed out to the Power Plants. Everything was in place; it was time to insert the first people.

The transmission was received at ground level to start inserting the living humans. Massive harvesting machines creaked to life, red eyes lighting up all across the field. Humans were scooped up from their containment cells and placed into long oval shaped capsules implanted into the side of huge cylinders. Once inside the machines would knock the humans unconscious and began the operation of inserting wires and connecters all over their body. Connecting their forearms, back, head, lungs, heart, and the nervous system to the Matrix system. Once they were wired into the system the machines sealed the capsule and initiated the Matrix. ............................ Jon awoke in a comfortable bed in a smallish apartment. He sat up very confused. He hadn't remembered falling asleep. In fact, he hadn't remembered being in an apartment.ever. On the other hand, he couldn't remember what the norm was, so he stood up and looked at his surroundings. A normal sized apartment complete with computer desk, chairs, small kitchen, and a bathroom. The usual commodities, but somehow it all seemed. fake. Oh well, he could find no reason for its fake feel, nor could he find any reason that it should be anything else. He grabbed his keys and walked out. The apartment hallway was definitely not new, but it wasn't quite run down either. It was worn, but it didn't seem genuine, the same feeling as his room. Jon couldn't shake the feeling but he still didn't have any good explanation of why it wasn't right. He walked to the end of the hall and stepped into the elevator, instinctively pushing the "B" button, almost as if he had been doing it all his life. The elevator hummed to life and opened upon the ground floor. Jon stepped out into an empty lobby. Weird, where was everybody? There wasn't even anybody behind the counter. Or was there? Now there was a man in a nice looking business suit standing behind the counter. He hadn't been there a second ago. had he? Jon couldn't remember. It seemed like he hadn't been there, but Jon couldn't explain why. The lobby also had a few people in it. Why hadn't he seen them before? Jon shrugged; he couldn't even remember why he was scared anymore. Everything was normal. ............................ "The humans are taking to the program perfectly."

"Just as I expected, the Matrix is populating nicely. Nobody notices anything."

"Congratulations Ms. Oracle."

"Thank You"

The machines continued to insert more and more people into the Matrix. The humans already inside didn't notice anything when someone would simply appear right in front of them. They couldn't quite seem to remember them not being there. It seemed like a foggy dream, real. but not real. They couldn't quite grasp what was wrong. Exactly the way the machines had intended it to go. The prison was working just fine, the humans were none the wiser. ............................ Jon continued his walk down the street. With every step he took it seemed that more people were out on the street. Weird, but not so out of the ordinary that it made you think twice. Jon strolled into a large office complex and scanned an ID card that had been attached to his belt loop. The door in front of him released an air lock and Jon walked inside. Had he always done this? It didn't seem like he'd ever been here before but it all happened so naturally, like he'd done it for years. Jon took the elevator up to where his desk was. He casually walked into his cubicle and saw his partner sitting hunched over his desk.

"What's wrong Neo?"

"Everything"

"What do you mean?"

"It's over. They've won"

"What's over? Who are they?"

"Do you remember anything? The machines, the war, the pain? You. you used to be a doctor."

Jon stood looking at his partner with the "what are you talking about" look on his face. Then, it hit him; he did remember being a doctor. In fact, he remembered the war too, and the all the pain even the evil machines.

".I. I do remember being a doctor. How did you know that?"

"I know everything. Do you remember the Matrix?"

Jon thought and vaguely remembered hearing something about a matrix.

"Sort of. yeah."

"I can see the Matrix; the Matrix code created by the machines. You are made up of code; you're in their system right now. This is the end of the war, the ultimate goal of the machines. You are trapped in a prison so they can harvest your energy and there is only one way out."

"How?"

"You must realize the truth"

"What truth?"

"This isn't real. None of this is real. Your clothes, your desk, your apartment, even your hair and your body aren't real. This whole city is fake; you must realize it if you ever wish to be free."

Jon plumped down in his chair and pondered this. He could distinctly remember being a doctor. He could remember the war with the machines. Now he could even remember being tortured and used in experiments. Jon concentrated and remembered being hauled up the side of a giant cylinder and shoved inside a metal capsule. He remembered the implants. Jon sat straight up, breaking through a thin red slime covering as he did. He was sitting in the capsule he remembered being forced into. He fought to breath against the life support jammed in his throat. He tore it out and took and deep breath of the almost toxic air. As his eyes adjusted to the light, Jon saw that he was atop a massive black cylinder, red pods like his own adorning the surface.

"The Matrix.has us." Jon's head fell into his lap and he wept. ............................

"Red Alert, one of the humans has woken up and his alive in our world."

"Damn that Neo. Put in the defensive measures. Secure the live the one."

A Squiddy scanned the Power Plant and found out Jon's position. Hovering up to Jon's pod he produced a laser from one of his tentacles. Jon looked up, despair in his eyes.

"Good Night, Human" the Squiddy croaked, just before firing a deadly laser into Jon's retina. Jon convulsed and then lay limp, hanging over the edge of his pod. "Only human."

*Long chapter, tried to explain a lot of stuff. Hope you aren't lost. Please review this! Sorry it took so long to get this up. More to follow.