Author's Note:

Ok, this is a new story, since my Crow project never took off, I'll junk it in favor of this one. To my readers of Heirs of the Warrior, do not worry, the next chapter is just ridiculously long. So I got inspiration for this after going through a few sci-fi books, and thought, 'How awesome would it be if someone could program a person? Like in the Matrix or something.' From there, I pretty much ended up combining that, some temporal distortion of some kind, and Naruto, and I have my story. I'm a huge sci-fi fan, so I'm really going to try to write something in that field, but it will be independent, all original. Look for it soon. This story I entitled "What are we really?" The main reason being is that throughout the novel, my OC main character will discover that chakra, being energy, can be controlled, and as such, a code of some sort must exist to govern it. He starts learning with the help of a certain medic kunoichi, and eventually, he figures out a method to literally program a human being. As a result of this, he and those his discovery affect have to re-examine what exactly they are, sentient beings with unique thoughts and feelings, or just programmable automatons that happen to be conveniently pre-programmed. As all this occurs, the main character is also has to question reality on an even more fundamental level, in the sense that being literally forced into an alternative reality forces him to question the existence, and even the relevance, of his own reality. I actually plan for this to eventually develop into an independent work, the basis for it being this. So, please enjoy this story, and please review.

What are we really?

Prologue

The admissions board read over the transcript again. It was flawless. His academics were all the most challenging courses available from the best school in his state. His standardized tests came back perfect, each one since the first one he took. His counselor even included copies of his grades for the entire year in each of his classes in a portfolio. Straight across the board, perfect scores. Community service records were impressive as well; his school had a remarkable engineering program, the projects of which were almost entirely focused on aiding people with disabilities, or helping the needy in some form. Each project met with remarkable success, some even being patented and put into production. Each project, for four years, he led each team.

"Unusual, isn't it, a high school engineering program of that level?" One of them asked.

"Hell with the program, think about the kid. He must be a machine. Christ, there isn't a flaw on here. Look at the program he wrote for a final project for his last Advanced coding class…it's insane. Our graduates don't do things on this level." One director pointed out.

"He made a video game. Graphics, sounds, everything. He spent a lot of money to get it done…hiring everything. Sound directors, music, etc. He did the majority of the work, a few friends jumped on to help with things other then the code. He wrote every bit of it himself."

"Honestly, where does he find the time?"

"Medical report. He's an insomniac."

"Ah…this kid really freaks me out a little…his interview was odd. He is insanely motivated at whatever goals he had, but in his opinion, nobody else has to know them. And another problem…his respect for authority is lacking. He's big on Thoreau and such."

"Psychology students couldn't do better then that?"

"They didn't find out a damn thing. Didn't you read the interview report? He said basically that, and then answered whatever questions he felt like answering. Others he just let go by, and gave the interviewer a freaky stare, as she wrote anyway."

"So what, he's a little odd? What are his relationships with the students, I think that is more important. We don't want any incidents."

"Oddly enough, he's almost universally liked. He acts completely different around some then he does with others, and does so by choice."

"Whatever, let's stick to the transcript ah?"

"Is there anything we haven't covered? I mean, let's sum this kid up. He has perfect grades in his core subjects, perfect grades in his electives and he happens to be incredible with languages, he speaks five. Spanish, Mandarin Chinese, Italian, English, and German. He is learning Latin, Greek, and Russian at the moment. And above all else…he's 16. He's in."

"Well then, Logan Reed, welcome to M.I.T."

Several months later, Logan Reed had already established himself as a leader among the students.. He always had his laptop on him, as well as bag full of note books. He had to get permission from the highest officials of the school to go over a double major, but he was allowed to attend classes for a Major in Electric Engineering, Software Engineering, and Hardware Engineering. He was getting a Minor in World Languages. His insomnia affected him little apparently. He really was unusual. One look into his eyes and you knew the cogs were spinning, pistons firing, and the boiler heating up in his mind. Always he was thinking about the possibilities of every thing he saw. It was in part what he developed insomnia because of. If there was anyone with the potential to do something nobody else did, it was him.

Today, he was working. He sat, typing line after line of line of code. 'I hate work.' He thought. It was the bane of his genius, that everyone wanted him to do something. All he wanted to do was relax, and let someone else fill their lives with worry. After all, he could basically hack a bank to get money, so that wasn't an issue. As far as he could tell, the only reason he was here was because he was still 16 and his parents could make him.

The blaring of security sirens drew him out of his hypnotic state. The grad students in the same room looked around to see what happened.

"Hey…you know this isn't a fire drill." Logan said as the three were running out the door. "It's the lockdown alarm. Someone or more likely several some ones have forcefully entered this building. As such, I would stay here."

The other students looked at him, and, realizing he was right, stayed were they were. It wasn't long before someone started knocking on the locked door.

"It's locked. Leave it." One man said. Logan breathed. Then one of the grad students knocked over a wrench.

"Fuck." Logan said. First he heard gunshots, then he realized they had shot the lock out. 'Security can't be far behind…maybe if I hide…' he was about to move into a cabinet, but a knife at his throat stopped him. He recognized the weapon. 'A kunai? There's an odd choice of knife.'

"Name." One of the men said.

"Jason." He answered.

"Hey, Jackal, don't they carry IDs on this side? Check his. Master will kill us if we fuck this up." From there, they searched him, found a driver's license, and then his name. They knocked him out and dragged him away.

Logan woke up in a cell. It was basic, a room, some bars, and no window. The first thing he noticed was the cell was guarded by five people. All of whom were dressed…differently. Not that he was one to care about fashion, but in his situation, anything could be helpful. The men wore what looked to be armor of some type. Looking around, he realized the room was lit by torches.

"Where the fuck am I now." He said.

"Ku Ku Ku…welcome to my country." A voice said from the shadows.

"Ku? You have one messed up laugh. Who the fuck are you…and what the fuck country is this, where you need torches…must be a real shit hole. And your English sucks by the way, but at least you speak it. Your accent…Japanese. But this is not in Japan…" Logan said. As Logan rambled, he looked about his cage. Then he saw the equipment. Boxes of it, enough to build virtually anything.

"Quite right on all counts. My guards can speak English as well, just so you're aware. By your reckoning, were not even on Earth. Let me get to the point of why we took you. You have a vast amount of technological expertise. I have made certain discoveries which have opened my eyes to a unique possibility, one which I need you to realize."

"Fuck you. Whatever it is. Fuck you."

"Don't force me to resort to torture. You'll find this world is far more barbaric then your own."

Orochimaru was the leader's name, and apparently thought that by creating certain components designed for organic integration, the human body could be infinitely manipulated. Logan was familiar with the idea, it had been proposed in books, movies, and other mediums. He would have refused, but he liked his fingers where they were.

Several weeks went by until Logan found his chance to escape. One of the guards was interested in what he was doing. As Logan studied and took notes, did sketches, and wrote programs, the guard watched him intently, trying to discern what he was doing.

"I'm writing the code that will govern the conduits that will jump the nervous system." Logan said, taking mercy on the poor soul.

"Oh yeah. Well keep at it." Logan smiled at that. This guard had no idea what was going on. That meant manipulating him was just a matter of being smarter. A little while later, Logan took out a welding kit and connected it up. He wasn't happy about what he was about to do, but it was necessary.

'I'm sorry about this, but I want out.' Logan thought. He called to his guard, who instantly looked at him. Logan walked to the bars. "Listen, your leader, he wanted me to construct an optical enhancement device, but in order to do that, I need a map of someone eyeball. Would you mind just looking into this end of this tool I have here? It should only take a second."

"It is for Orochimaru…" The guard leaned in. His eyeball didn't take long to burn through. The extreme heat of the welding torch boiled it into nothing. The skull took a few more seconds. Then the brain…the brain sizzled. Like frying bacon. The guard never got the chance to scream before his nerves were shot and he went into shock. He was dead soon after. Logan cut open the bars.

"Sorry dumb ass." Logan said, not looking at the body. He was sick to his stomach, but he ran around. He found a door, unlocked, soon after. He doubled back to the cage, grabbing everything he had built. His notes, his laptop, schematics, and any useful part he could grab. He took a few minutes to look around. In the back of his cell was a large, very heavy unopened box. He checked it. It read: "10HP Tecumseh Engine; Part# 210112A". Logan laughed. "Could these guys be dumber?" Logan spent the rest of his night assembling what had to be the worst go-kart in history out of anything he had available. He finished around four and drove right out of what was apparently a single-prison compound. He kept driving well into daylight, thankful that they had no idea what he could use to escape, and happened to bring back some gasoline.

Orochimaru was furious. Logan Reed was key to his plans, and the genius had managed to build himself a method to travel easily ten times faster then anyone shinobi he could send after him. Worse, he somehow managed to pick the direction of Konoha. It would be a matter of time before ANBU had him. Then a new fear dawned on him. Logan was making real progress on his work. With the help of some of the best medics around, as well as an ideal test subject, he would succeed. Those would be provided to him by Konoha if he revealed the project to them.

"Sasuke. Find him, and bring him back, alive. He is after all key to your development."

"Done." The cold hearted Uchiha answered.

Uzumaki Naruto was patrolling outside of Konoha. And he wasn't happy about it. Patrol was a crap job, and the only perk of being a Genin was that he shouldn't have had to deal with it. But Tsunade thought that his tenure at that stage was over. After 3 years of training, he was at least high chunin. But today Uzumaki Naruto would have an interesting experience. He heard the roar of what he didn't realize was an engine, turned around, and barreling toward him was a giant metal monster. It hit him, and he went flying. The beast stopped.

"WHAT THE HELL!? You are DEAD." Naruto said, preparing a Rasengan. To his surprise, someone got out of the thing. Logan noted that the emblem on his new friend was not the same as that of his captors.

"Look, there was a misunderstanding. I got dragged to this third world piece of shit country by some sketchy looking guys who dropped me. Called themselves the 'Sound' I think." Logan said. But he said it in English. Naruto, not knowing how to respond, knocked him out.

Logan Reed woke up a little while later in another jail cell. 'Damnit!' Was his first thought. Then he remembered that Orochimaru spoke Japanese.

"I don't speak it…but the laptop does!" He shouted out. He whipped out his laptop and a case filled to the brim with flash drives for every possible subject. He earned a reputation as the campus research man. He dug one out labeled Japan. He called up a dictionary program stored on the drive, and ran it to translate a basic paragraph. He typed:

There has been a misunderstanding. I was kidnapped by some people called the Sound, led by Orochimaru. I built that kart, ran away, ended up here, and hit that guy. Sorry about the mix up. Now let me the fuck out of here, or let me speak to someone who can.

The laptop apparently translated it perfectly. In a few minutes, he was being dragged through a building escorted by two sketchy guys in masks. "Is everyone here a freak?" He openly asked. He brought into a room with big doors, broken walls, and much screaming. The blonde boy he hit was being thrown into wall after wall, yelling the whole time. This was being done to him by the hottest woman he had ever seen. And probably the scariest. He just dug out his laptop and typed away.

I don't speak your language, but this can translate for me. I have another keyboard available for you…that's the thing with the keys. Hit them to enter a message. Allow me to explain who I am…my name is Logan Reed, I'm 16, and I just spent the better part of three days not eating and running from some crazy guys who call themselves the Sound. Then I make it over here, hit the blonde kid because I thought he was one of them, and then he got the jump on me.

He had to wait a bit for Tsunade to stop killing Naruto before the guard starting talking, and he was allowed to show her his message. Logan plugged in and laid out a key board with Japanese lettering on it. He had one for every language on him. Tsunade understood immediately.

Why did Orochimaru kidnap you?

He had this insane human alteration project. He needed my help to build and program the machines that were the basis of the project. I have all the data I collected, as well as his.

That sounds like something he would do. Logan, I hate to tell you this, but if he claims he dragged you from another world, then he probably did. Orochimaru is one of this world's most dangerous individuals. How did you, an untrained civilian, make it out without getting caught?

His guard was a moron. I…I used an extremely hot torch device called a welder and burned right through him. Then I used the torch to cut the bars on the cell. The facility I was in was secluded, no power, and only one guard at night. Of course, on foot I would have been caught in no time. With that kart I built, it would take a miracle to catch me.

This is the village of Konoha. I'm the leader, Tsunade, the Hokage. The Sound is one of our foremost enemies. Sorry about Naruto by the way. He tends to be a little compulsive. He is one of our best shinobi however, or at least will be.

Shinobi? As in ninja?

Of course…your world doesn't have them?

No. Anyway, I appreciate the hospitality. I would like to point out…Orochimaru's project might be nuts, but it could work, just not in the way he thinks. The components he wants built don't need to internal or even separate. His files went on and one about some kind of energy naturally generated by the body.

Chakra. Shinobi focus it to perform techniques.

So it can be manipulated?

Of course it can.

Get me a notebook and the best doctors you have. If I'm going to be here, I might as well use this projects data to help you guys.

You want to work for us? Why?

Simple. I have a condition of sorts. If I realize something is possible, I have to see it done, or at least help. I hate that part of me, because I always end up with a hell of a lot more stress then I like. Nonetheless, there's potential here. Besides, if I have a chakra system, I might be able to fix myself.

Since you're new to our system, just prepare me a basic file of what you want to do. I'll think about it. Thank you for the information about Orochimaru. Naruto will escort you to a place you can stay. He'll be your guard for the time being, and will escort you around Konoha.

I'll have a report ready by tomorrow. Do you want a medical report on myself as well? For doctors or something?

You have one?

Long story, but yes, I have the information from my most recent physical.

Then yes, please. Welcome to Konoha, Logan.

Next time we meet, I will thank you in your language.

THIS STORY IS POST-TIMESKIP