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#Disclaimer: See chapter one.

After many hours of working Smith stands up from the desk and looks over at his creation of a new Rouge Program. With a few final minutes of typing the program awakes. " Go!" Smith commands the program.

The program codenamed Sky nods and with out a word takes off into the matrix.

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Trinity looks at him with a mixture of shock and horror on her face. She sits there watching him for a moment trying to find words to comfort him. She sighs quietly.

" What's wrong Trinity?" He looks at her with a mixture of concern, compassion, and worry on his tired face.

Trinity manages to smile at him and pushes away her worried thoughts behind a wall that usually blocks her emotions from all others. " Nothing.. I was just thinking about something. You need to sleep."

He stands up and shakes his head. " I already told you I can't sleep.. More dreams will haunt my sleep and keep me awake, and besides its time to get up anyways. Soon we will be going into the Matrix."

She looks at him and stands up as well. " Neo no you can't go into the matrix like this. Especially with that Program running around. We don't know what it is capable of."

He sighs knowing she was going to say that. " Trinity listen.. Nothing is going to happen I won't let go. I have to go into the matrix and face this thing though."

Trinity sighs knowing he won't listen to reason since he set his mind to do this already. She walks after him as he starts to walk towards his chair.

" What are you doing?"

" What does it look like Neo? I'm going with you. You're going to need my help." Trinity tells him stubbornly.

Neo sighs knowing by now protesting with her when she has her mind set on doing something is a lost cause.

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They enter the matrix and shortly after Sky and Smith walk towards them. Sky at once heads towards Neo and begins the fight. Smith meanwhile was a mere distraction to Trinity to keep her away from interfering with the fight.

Neo fights for his life as he avoids punches and kicks from the program. A kick sends him flying back against the wall of a building.

The program walks over with an emotionless expression on its face and stands over Neo.

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Morpheus meanwhile was on board the Nebuchadnezzar working on a computer researching information that would help in solve the mystery. As he works every so often he glances at the Matrix. One of the crewmembers was acting as the operator since they didn't have a new one yet to replace Tank. Morpheus raises an eyebrow finally understanding what was going on. " Interesting..." he says to himself as he gazes over at the matrix.

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The fight meanwhile was definitely not going in Neo's favor. The program ruthlessly batted him around with ease. Sky grabs Neo and flies up into the air. He throws Neo down towards the ground.

Neo flies down to the ground at incredible speed. He watches the ground rush towards him helpless to do anything to prevent it. He hits the ground hard and moves no more.

Trinity breaks free of Smith's grip and runs towards him. She drags his body towards and exit and they soon leave.

Sky starts to follow them but Smith puts a hand out signaling him to stop. " There will be another time to finish the Job."
Sky nods as Smith brings him back towards their base of operations.

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Massive bruises and a few broken bones were Neo's injuries. When he wakes up back in his in his bedroom on board the Nebechadnezzar Trinity and Morpheus are standing in his room. He looks up at them and smiles. His memory has been recovered and he had forgotten about the battle with the twins and about the Program. For now he just sits there resting from his injuries not knowing how he got them or he was even in a fight.

Trinity smiles back at him and says. " Get some rest I'll be back in a little while." She then walks out towards the mess hall to ensure that Neo won't hear her and Morpheus's conversation. She takes a seat at the table and waits for Morpheus to begin.

Morpheus looks at her as he sits down on the opposite side of the table from her. " The virus is the answer to all of the problems, and that is how that program was created. Sky as it's being called was made from the virus that had infected Neo. Every time he went into the matrix he suffered because of the virus. The virus took some of his coding and replicated it. The replication then got transferred to another computer until it was complete. Now that he has his memory back he won't remember the things that happened back inside the matrix during his state of confusion. Through the virus the program, Sky, and Neo are connected. He will remain with the virus until Sky is freed. He can't be destroyed, but since he has a human side to him know he can awaken and become a valuable ally to us in this war, but that will take time. No one can tell him other wise he must awaken on his own. When the time comes we must be ready for the other programs of the matrix will hunt him down."

Trinity stays silent through Morpheus's explanation. " What about his injuries?"

" Those will heal rapidly due to the strange connection since Sky was the one that did that damage." Morpheus gets up and walks away to brief the new operator, Link.

Trinity remains there at the table for a few moments before she walks back towards Neo's room. She sits down on the bed next to him and falls asleep shortly after.

Neo meanwhile drifts off into once again troubled sleep. He dreams about Trinity.

A/N: This is the last chapter in the story, but a sequel is in the process. Than you all to have reviewed and offered kind words in this story.

Reviewers:

Divamercury: Here is the final chapter of this story glad you liked the rest of the story.

Elenillor: Than you for the kind words. Here is the final chapter of the story.