The Matrix: Reborn

This story is a fan fiction that takes place after Matrix: Revolution. The storyline is written by Kuro Selas and completely disregards the Matrix: Online.
==Chapter 1 - The Matrix==
"Have you ever stopped to think if anything that surrounds you is in fact real? What if this was all just a dream you couldn't wake up from, will you be able to tell the difference between dream, and reality?
For years, the Matrix has prevented us from seeing the truth. "
"And what is the truth?" - A voice that was somewhat familiar to Morpheus stopped his speech. In front of him there was a young man in his twenties, with dark hair, and dark eyes, his face made Morpheus remember someone he had lost years ago, someone that ended a war that had last a century, a man known as Neo. He was the savior of both mankind, and machines.
"The truth is that you are all slaves in this world. The matrix is a way of control, a type of control we cannot see or touch... But you better see it for yourself."
Morpheus left the dark cold living room, and stepped towards the balcony, looking over the city.
“And how are you supposed to do that? How are you supposed to show me the truth?"
Morpheus looked towards Rei.
"You have two choices. In my right hand I hold a red pill, this pill will bring you one step closer to the truth, and in my left hand, I hold a blue pill, which will make you forget everything about our encounter, you will wake up in your room like you would have done in any other day"
Rei wondered for a second, how far would he go to satisfy his thirst for knowledge? He gazed upon the pills that were in front of him, and stretched his hand to reach for the red pill.
"Remember, the choice you are about to make is irreversible, you will not be able to go back once you make it.", said Morpheus as he looked deeply into Rei's eyes.
Rei took the red pill, and swallowed it. He felt his heart beating faster, and his head seemed to about to explode. He felt like the world around him was overwhelming him, holding him in chains, suffocating him, until suddenly he felt nothing, everything around him disappeared, and he felt like he was waking from a long sleep. Suddenly Rei felt himself drown in a strange pink liquid, he gasped for air as his pod opened.
For the first time in his life, he saw the real world. It was very different from the world he knew, the grayish surroundings were not what he was expecting, was this the truth Morpheus had promised him, was this what he choose to see?
A mysterious robot descended upon him, disconnecting the wires attached to his body, and dumping him into the sewers below. He tried to swim, but his muscles were totally useless, because they had never been used in the real world. Before he drowned, Rei was rescued by a craft floating above him. Aboard the ship, he was welcomed by Morpheus, like so many others were before him, before he blacked out. The Matrix was no longer the prison it once was known to be. Now those who wished to be free were cut loose from the system.
The machines still created humans as a means of survival, but they no longer cared for those who were taken from the system, this was the only possibility of peace for both parts. There's was a limit though, they could not free everyone, or else a new war would break out, instead they would only release those who had the potential.
Time passed, and Rei was removed from intensive care, his body was treated so he could survive in this new world. His head was filled with doubts, and questions. What happened to this place? Why am I here? Am I dead?
==Chapter 2 - The Nyx==
Morpheus former ship, the Nebuchadnezzar, had been destroyed years ago, they were now aboard a ship called Nyx, commanded by Morpheus, and Niobe. The Nyx was a little bigger than the Logos, but it was still very fast. The crew was composed by Kid, Link, Ghost, Niobe, Morpheus, and the small child Sypilos, Morpheus', and Niobe's son.
Rei was approached by a young figure by the name of Kid. Years ago, Michael Karl Popper, also known as Kid, saved Morpheus, and Niobe by blasting the cable holding the gate to Zion, allowing the Mjolnir to enter, and activate its EMP, winning the first round of the battle. After Neo's demise, Kid was trained by Morpheus, and proved to be quite the student.
"Shit, you really look like him."
"Like who?" - asked Rei.
"Neo, haven't you ever heard of him?"
"The hacker Neo? I thought he died years ago."
“Well, we aren't sure of that yet. Morpheus still thinks we can find him. You bear a great resemblance to him, and yet you are so different."
"What happened to him?"
"The only thing we know is that he stopped the war between man, and machine, and after that, he just disappeared. We've been searching for him in the new Matrix, but he seems to have just disappeared"
Rei still didn't understand what the Matrix was, so Morpheus decided to show him. They went inside the Construct, in order to fully illustrate the concepts, and known origins of the Matrix. Morpheus told him about the war between humans, and machines, and about the last human city, Zion.
Rei was overwhelmed. He had been trapped inside a world that was never real for years, and he did not notice how something like that could happen?
Later, Link, the operator of the ship, invited Rei to begin his training. That day, Link digitally uploaded various fighting styles into Rei’s memory for several straight hours.
"How is it going Link?" - asked Morpheus as he entered the room.
"Well this guy is like a sponge, he's been absorbing data for 8 hours straight with no rest"
"That's impressive" - said Kid as he approached Link.
"Upload the Sparring program Link, I want to test him."
"Are you sure Kid? Normally Morpheus is the one that..."
"No, let him go this time. This should be interesting." - said Morpheus interrupting link.
"Uploading both into the Construct's Sparring program."
Within the Construct's Sparring program, Kid approached Rei.
"Impressive isn't it? This is a sparring program, similar to the programmed reality of the Matrix. It was built under the same basic rules. Rules that are no different from those of a computer system. Some of them can be bent. Others can be broken. Are you ready for some real training?"
"I thought you would never ask."
Rei took an offensive position, and taunted Kid.
"Getting cocky I see, well let's see how you handle yourself."
On the Nyx, the news broke of the digital duel, the crew aboard hurried to watch the two fight. Kid was considered a prodigy, taking his inspiration from Neo, he had achieved greatness. To their surprise, Rei's movements were fast enough to hold his own fairly well against Kid, but since Kid had a free mind, he got the upper hand on Rei, who dropped on his back after Kid sent him flying with a flying kick to the chest.
"Not so cocky now, are you?"
"You're way stronger than me, I can't beat you."
Kid smiled as he remembered himself saying the same thing when he fought Morpheus.
"Why do you think I'm stronger? You're larger than me, and yet I was able to kick you way.
In this world, our body is controlled by our mind, by what we know we can do, the laws of physics do not apply in here."
Rei got back up, and took a fighting stance once more.
"Again?" - asked Kid.
Rei nodded his head, and the fight broke out once more.
"What is that?" - asked Link as he watched the monitors.
"His neuro-kinetics are amazing." - said Ghost.
"It's impossible, it can't be." - said Morpheus as he saw Rei's movement speed approach the movement of his former friend.
Rei's movement was much faster, and he was almost able to beat Kid who dodged a fast shadow kick, and grabbed Rei's leg, sending him against the wall.
Glad to see Rei’s mind was becoming free, Kid told Link to load the Jump program.
Rei, and Kid were now on the top of a tall building looking over the city.
"You have to let it all go, Rei. Fear, doubt, and disbelief."
"What if I can't?"
"I know you can. Neo, was known as The One. He was able to break the rules within the system like no one else had done before him. He was able to fly faster than any airplane, and stop bullets, and he started just like you are starting, with doubt, and fear in his heart. I heard he failed the test you are about to take, but I believe you will not fail. "
Kid demonstrated the ability of a free mind by leaping from one building to another in a single bound, and Rei was amazed by such a display.
"Ok now. There is nothing to be afraid of. You can do this" - Rei spoke to himself while trying to calm down.
Rei leapt really high, and just as he was about to reach the other building, he started falling, but before he fell, Kid was able to catch him by the hand.
“That was really close, in fact I don't think I've ever seen anyone get so close to the building in the first jump"
The crew of the Nyx was overwhelmed by what they saw. It seemed that Rei held an amazing potential. Was he the new "One"? Was he Neo's descendant?
Back in his body, Rei learned through Niobe, that the body cannot live without the mind. If one dies in the Matrix, they die in the real world, so he must be careful within the program.
Morpheus took Rei through the Agent training program, demonstrating the danger of those who have not yet been freed. Rei learned of the fatal encounters with agents, and their amazing abilities within the Matrix. Morpheus told him that the One was the only man who had ever defeated an agent while fighting one-on-one. Agents preoccupation now was to prevent those without the potential to be freed. They acted like safe keepers. Although man, and machine lived in peace, agents were still considered a menace, since their function was to eliminate anything, or anyone that could reveal the truth of the Matrix, or cause harm to its virtual reality, this means that although minds could be freed from the Matrix, minds without potential could not witness events that would harm the Matrix reality.
==Chapter 3 - The Machine Graveyard==
The crew was having dinner, until Link stepped in, and spoke to Morpheus.
"Sir, we have news from Zion, it seems there was some a problem with one of our ships, the Traveller has not responded to any of the communications from Zion, they are asking us to search for it."
"What's its last known location?"
"The machine's graveyard."
"The machine's graveyard?" - asked Rei "What's that?"
"Like the name suggests, its where the machines send their malfunctioning members. It's a dangerous place were threats appear around every corner. I don't know what madness drove them there, but we have to go to their rescue." - said Niobe just before she got up from the table, and headed for the pilot cabinet.
Rei wondered what type of perils would be present in the machine's graveyard, he went to his cabinet, and tried to get some rest. He had been training like a lunatic, always trying to surpass himself.
The Nyx arrived at the machine graveyard two hours later. Everyone wondered what would they find there. Not even Morpheus, the oldest of the crew had been to such a place. After turning their spotlights they entered the graveyard.
"Not the best place to have this spotlights turned on." - said Ghost with a concerned tone in his voice.
"It's the only way we can find them. Niobe..." - before Morpheus could finish the alarm sounded. It seemed something terribly fast passed really close to the ship.
"What was that?" - said Rei.
"Was that an Assassin?" - asked Kid looking at Morpheus.
"Niobe, get us out of here!" - shouted Morpheus just as the alarm sounded again.
"What's an assassin?"
"It's a killing machine, they're really ancient and really dangerous. They are two times faster than sentines and three times deadlier." - answered Kid while Rei tried to catch a glimpse of the machine through the pilots window.
Speeding through the grayish walls of the cemetery filled with mechanical parts they catched a glimpse of the Traveller in the distance.
"That's the Traveller shouted Ghost as they approached the ship."
"What do we do Morpheus? The ship as clearly been taken down, the chances of finding survivors is almost zero." - asked Niobe as she avoided another assassin. 
"Take us as close as possible to the Traveller and fire an EMP to destroy the assassins near it. " - said Morpheus as he analysed the sittuation.
Niobe drove as fast as possible towards the Traveller and at Morpheus signal Ghost fired the EMP taking down every assassin that surrounded them.
"That should be enough to buy us some time." - said Kid.
Rei was amazed by what he just saw, Niobe was simply an amazing pilot.
They made their way into the Traveller, the silence that surrounded them gave them all a chill. Entering the Traveller they saw something that they never expected to be possible, the crew was alive. Only Mak, the crew's operator had died in the rough landing after they were taken down by an assassin. 
"Morpheus!" - the voice of Capitan Raja, son of Ajax, was well known by Morpheus. Although Raja was really young he made his way into capitan faster than anyone before him. Problably because of his father's death in Bane's EMP discharge, Raja was tried really hard to become a capitan.
"Xaja! Is good to see you again my friend!" - said Morpheus as he hugged the young capitan. " What happened? Why have you come to such place?" 
"We were being followed by a strange Hovercraft, we tried to make contact but they only responded with fire and drove us all the way to this forsaken place." - said Raja
"A hovercraft? You mean it was one of ours?" - shouted Kid displease with the idea. 
"Not one of ours, it was one of them... the Red Matrix." - whispered Raja, as if he was speaking of the devil.
"Red Matrix? What's that?" - asked Rei.
"They are humans who fight to destroy all those who seek to reveal the truth about the Matrix. Not all humans wish to be free from the Matrix and leave in this world. They chose dream instead of reality, and they are willing to kill every last one of us to suceed." 
It took two hours but the crews of both ships managed to get all tehy could from the Traveller into the Nyx. The Traveller could not be fixed, at least not in there as they would be risking their lifes to do it. Instead they would all escape that place using the Nyx.
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