Listen, readers, I'm really, really sorry. Here's what happened:

I was planning on updating this story shortly after last time. However, schoolwork came up and I was forced to wait a week before I actually had any free time. Of course, as soon as I planned on writing another chapter, the shit hit the fan. Everything in my personal life just exploded in the worst possible manner. So, after a long time, I finally came back to the story. Looking over it, I felt that I wasn't doing it quite the way I wanted to, and rewrote it as you see below. One of my favorite things to do is to ponder as to how things in the Naruto universe work, at a scientific level. Well, I thought that the "Academy Three", as I've decided to call them, might be the best techniques to start with. If you check my profile, you'll see my ideas on what chakra is, as well as how Katon (fire release) techniques work.

I'll be deleting the other chapters soon after posting this.

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A certain blonde boy cowered within the bottom of the closet in which he kept the single orange jumpsuit that he wore everywhere. Currently, though, it was on him. He needed to be able to get up and run at a moment's notice. It was there in that room that he planned to sit for twenty-four hours, without food or water, with his eyes closed. All he could do was hope and pray that he would survive his fifth birthday. Unfortunately, though, Naruto knew enough to know the terrible truth: he probably wouldn't. He would try to stay on his toes, but he really wasn't as concerned about living as he once was. He let all of his worries slip away, and instead focused intensely upon the task ahead of him. He would try, but he really didn't care any more.

After the first few hours, Naruto was not able to stay alert; though he certainly wouldn't be falling asleep, he eventually found himself drifting within himself. He didn't know how he had done it, but suddenly his mind, his consciousness, found itself in a trance-like state. It felt to Naruto that he was floating inside his own body. He could hear, feel, see, smell, even taste everything with a sudden sharpness, and yet it was all so distant, so easy to forget. It was in this state that Naruto spent many more hours.

Here, in the empty void in which he was suspended, things seemed clearer. Such matters such as once seemed so puzzling and illogical—such as why the Hokage so rarely came and saw him—seemed to come into focus. All of his knowledge, bits and pieces of information that he had gathered, seemed to coalesce and form coherent ideas. It was in this dreamlike state that Naruto came to realize something, with absolute clarity. It was something that he had never noticed before: he was smart. Very smart. In all the time that he had spent running, he had never been able to stop and think. In all of his life, he had never been able to forget his troubles and to apply his mind. And now it seemed to him that he had accomplished that task—and by complete accident, too. It seemed that the villagers' vicious attacks that had ruled his life for two years—since he was thrown out of the orphanage—had finally yielded some positive results.

It was some time after he had this epiphany that Naruto felt something begin to tug on the edges of awareness. It was his senses. But he didn't want to lose this heightened sense of understanding. If you couldn't see things clearly, then why want to see things at all? With this thought, Naruto retreated within himself. The tug became harder. Naruto retreated even further. The hard tug became a pull, a scream, a shouted warning. But Naruto refused to listen. He dove further and further within himself. Suddenly, his senses portrayed to him the sound, sight of a door slamming open. The smell, that of polished metal and a strange man. Now scared, Naruto dove so deep within himself as to forget his senses, forget his danger.

Suddenly he came upon something, something that seemed to reach out to him, to bubble up through him. What rushed through him now was something incredible. Naruto saw nothing in his meditative state, but somehow he felt blue, wondrous blue, rushing up through him. The sense was euphoric. He felt as it rushed out of every pore in his body, protecting him. No, not so much protecting him. It was him. A much a part of him as anything else. Naruto didn't know how he knew this, didn't even recall puzzling this out or learning it in any way. He just knew, knew that he just knew, and knew that his knowing was something he shouldn't question, something that just was. Naruto felt the blue continuing to rush out. He could feel it slice up the man with the polished metal that had slammed open the door to his closet. The blue was a part of him, and extension of everything he was. He felt as the blue ripped through the doorframe so as to thoroughly destroy the man. He felt as it ceased its forward advance and instead began to swirl around the man. And he knew when it was done, when the man was gone, utterly destroyed. And with the man, the blue went too. And yet it didn't. While the blue that had attacked the man was gone, there was thousands, many thousand times more blue within him than that that had killed the man that surely would have killed him. And with the comforting feeling that more of the boundless energy was there to protect him if he needed it, Naruto resigned himself to leave the trance.

He opened his eyes.

Looking out of the closet, he saw what he had felt through the blue. The doorframe of the closet was in shreds, naught but scraps of wood hanging from stained drywall. The ground in front of him—up until about two feet in front of him— was also beaten, scratched, and deeply gouged. What he had felt was right about one other thing too. The man, the man that he knew had been there beyond a shadow of a doubt, was gone. Not as though he had left, but as though he had vanished, wiped off the face of the planet never to be seen again. All of this flashed through Naruto's mind in a time so short it was incalculable by even the greatest of man, or even the greatest of machines. And with the lightning fast observations, those that normally would have taken him seconds, came the reassuring fact that the intelligence that he seemed to have unlocked while in the closet was still there, still accessible. It was still the analytical powerhouse he had found it to be in the hours he had spent using it, the key to understanding so vast that he would comprehend in seconds what would take some of the greatest minds in Konohagakure hours, days, maybe even years to understand fully. And with this reassurance, Naruto wore something that he hadn't worn honestly as long as he could remember.

On Naruto's typically somber face was a smile.

Naruto walked out of the front door with that smile gone, now replaced with a stoic expression. Ahead of him was a task that he knew for certain was quite daunting. He needed to control his chakra, which he had recognized as chakra shortly after using it. And somehow, he knew that obtaining perfect control would take him a while. It might be the first time for a long time in which his new intelligence would fail him.

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Naruto was in the middle of a clearing in a forest, on his twelfth hour of trying to control his chakra. It was coming along swimmingly, though, and he was finding that as long as he focused, it wasn't too difficult. The first hour had been spent trying to consciously tap into his chakra, but once he had, he found that he could feel it, permanently within him, a vast ocean of power bubbling just below the surface of his skin, itching to be released. Though Naruto found it quite easy to resist this urge, it felt wonderful to let the power out. The only problem that he found was that there was a great deal of energy within him, so much so that he was completely unable to let out less than he had used against the terrible man when he first tried to release it. This amount, though, quickly tapered over the next eleven hours. Now, Naruto was having trouble releasing just a tiny amount. Anything even slightly over this threshold seemed child's play to him now, but that one point seemed fiendishly difficult to overcome. This was actually fine for Naruto. He was able to realize that without his new intelligence and focus, he would be completely unable to manage to let out what small amounts he could now easily use, even with years of practice. Though he would never give up, there were some things for which persistence couldn't help you with; like focus. After three more hours of intense work on the part of Naruto to release less than that invisible barrier he had seemed to reach, he decided that it was a lost cause. Instead he had focused on trying to let out exactly as much as he wanted too. Though for the first hour it would take him four or five tries to get fairly close to the right amount—in the range that he deemed "acceptable"—after a few more hours of work, he could get it exactly right, on the first try, almost all of the time. It was after this that Naruto began to feel a bit hungry.

With a sigh, Naruto turned around and headed off towards Ichiraku ramen. It wasn't his first choice for a meal, but with the very small stipend that the Hokage gave him, it was the only place he could afford. After all, it was the only place in the village that didn't overcharge him in any manner. Besides, he could eat a lot at once. That way, he didn't have to come back three times a day, and run a greater risk of running into the villagers. He stopped dead in his tracks as he thought this. Oh my, I really am pretty smart now. I never thought about it like that before!

And, with that, Naruto headed over to Ichiraku ramen, far less excited than he had ever been to go and eat there.

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Over the next week, Naruto worked tirelessly towards perfection of his control. After putting in twenty hours a day, he now found it quite simple to release any amount of chakra he wanted, regardless of the amount, from any part of his body. Except for any amount smaller than that barrier he had encountered earlier—he still found that impossible. What's more, he had discovered something else that rather pleased him. Unless he released as much as he had accidentally released against his would-be assassin, there was no noticeable drain on his reserves of that wondrous energy. And even when he did release that much, the drain was so small, he felt that he could do it a hundred times over without too much effect on himself.

It was while thinking about this, at the end of that week, that he realized there was much more he could do with chakra than simply release it in controlled bursts. He knew about jutsus, but he did not know how they were performed, apart from the hand signs that more or less everyone knew about. But when he had released his chakra to protect himself, it hadn't flown wildly out of him, it had spun out and surrounded the man. That in itself told him that it was possible to manipulate the shape of one's chakra. But what's more, there had been cuts all over. That told him that it was possible to change the properties of one's chakra. So, if he could do it unconsciously, shouldn't he try to do it on his own, while conscious?

And so it was that he began to attempt to control these two parts of his chakra. Over the next month, he found that by imagining the chakra as sharp, razor sharp, he could use it to slice through things, as though it were a blade. And just as though it were a blade, the harder and faster it was applied, the more damage it did. So after first getting the knack of envisioning his chakra as sharp, which took a whole two days to do perfectly, one hundred percent of the time, he began to learn not to simply release his chakra, but to "fling" it.

By jabbing his hand forward and releasing his "sharp" chakra he could put rough holes partly into trees, though only when he was close. He worked on this tenaciously, discovering through trial and error that he could use a small burst of chakra within his body to "propel" the chakra forward. Furthermore, he could release the chakra from only a fingertip so that it was naturally more contained, resulting in a small, clean hole that penetrated deeper than the rougher, wider one. When combined, these two discoveries allowed him to, at first, put a hole one quarter of the way through a small tree. However, after a week, he was able to put a same-sized hole all the way through a same-sized tree at a hundred yards.

What he moved onto next was very similar. Instead of jabbing his hand forward, he began to instead swipe it, as though is very fingers were blades. By continuously releasing his "sharp" chakra, as well as using an equal amount to "push" the chakra forward, he was able to cut paper-thin gashes into trees. With a week of practice with this, the paper-thin gashed could cut all the way through the tree from twenty yards.

With a little more than two weeks of "elemental" chakra manipulation practice under his belt, he moved on to the other thing that he knew was possible to control; the shape of his released chakra.

At first, he attempted releasing chakra in bursts, and controlling that. But he quickly realized that that was not working—once the chakra was out of his system, he could not give it purpose.

Then, he attempted to form the chakra into a sphere as it left his hand. After five hours of tiring practice, he finally got it to work, but the results were disappointing. All he got was a pale blue ball floating in his hand. It did not do anything though, and when touched it dispersed itself.

Seeing that yes, he could change the shape of his chakra, he decided that doing something else with it would probably work better, so he did. He tried to make it spin, like it had when it had defended him. After forming it into a cohesive sphere, he found this easy. In only ten tries, a thin strand of dark blue chakra was spinning in wild circles above his outstretched palm.

Excited by the results, Naruto did what any smart, inquisitive person would do. He experimented.

Slowly, he extended a finger from his other hand to touch the spinning chakra. When it made contact, he bit back a startled yelp as he let the his chakra scatter into the environment.

The chakra had hurt his finger, almost like it was a tiny fist hitting him at a million miles an hour. A grin spread across his face as he processed the implications of this with lightning speed.

Quickly he tested his idea. Instead of releasing just one strand, he released many. Then, trying again, he released many more. Each extra one made it considerably more difficult, but with practice and time, and twenty hours, he managed to form his wickedly spinning chakra into a sphere. Then, curious as to what it would do, he dove at a tree, driving the spiraling ball into it. With a crack, the bark crumbled and was ripped away, before the pressure on his attack was too much, and the technique forcibly released itself.

That devious grin spread across Naruto's face again. After some short hours of rest, he was up and at it again. Over the next few days he added more and more threads, in a smaller and smaller area. Slowly but steadily, the amount of chakra in the ball increased, until the color of it went to a sky-blue composed of thousands of threads to a navy blue that almost seemed to be, and almost was, one solid sphere.

For the second time, he ran at the tree, curious to see what would happen on contact. And my, was he surprised.

Unlike last time, the bark didn't buckle before being ripped away. In fact, the effects were more or less instantaneous; the moment the ball hit, bark was torn and flung in many directions, as the ball maintained its stability. Small amounts of liquids were thrown everywhere as he pierced the center of the tree, the hole he was creating expanding as flying sawdust ripped it open, essentially sandblasting it. And then it was over.

A second after hitting the tree, Naruto's arm pierced the other side, covered in water, sap, sawdust and blood. Despite his arm being stripped raw by the flying, uncontrolled, incredibly fine shards of tree, Naruto was immensely pleased by the results. Deciding to call it quits, he staggered back to his apartment, preparing for the day ahead.

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Naruto had awoken early that morning, walking without haste to a small hot-spring he had discovered one day while walking home. Hidden within a dense thicket of trees, and a few miles away from nearby buildings, it was a perfect place to wash off, his apartment's water supply having been cut off the day he moved in. After all, he wanted to look nice for his meeting with the Hokage today.

After spending a good thirty minutes in the cleansing water, he headed back not to his apartment, but to the Hokage tower. In an hour, he was there.

He entered the waiting room, admiring its spartan nature. The Hokage saw no need to flaunt his power and status.

Walking up to the secretary, he ignored her glare and asked politely, "Is the Hokage available?"

She seemed to bite back a bitter reply, and spit out what the Hokage had probably told her to in the event that Naruto dropped by. "Yes, just head right on up."

Naruto thanked her and walked up to the Hokage's office.

A knock on the door and a quietly spoken "Come in," and he was inside.

As Sarutobi Hiruzen looked up from his paperwork, he allowed a smile to spread across his face. He enjoyed Naruto's company a great deal.

"Ah, Naruto, it is good to see you again! It's been over a month since the last time you visited me!"

Naruto hesitated a moment before his reply. He hadn't thought of that. He had been so absorbed in his training that he had forgotten about the old man! But in spite of this, he was still quick in his response. "Sorry Gramps. But I've been doing some serious thinking."

"Oh really? What about?"

Naruto grinned. "Gramps, I wanna be a ninja!"

The third Hokage sighed. He had known this day would come. After all, the son of the greatest shinobi ever was more or less destined to become one himself. But he needed to be sure that this is what Naruto wanted to really do.

"Well Naruto, how sure are you about this?"

If it was possible, Naruto's grin grew even more. "More sure than you'd ever believe, Gramps!"

"And you know what that entails?"

"Yeah! I get to kick bad-guy ass!"

The seemingly decrepit old man chuckled softly. He would learn in the Academy exactly what being a ninja really meant.

"All right Naruto, I'll have you enrolled in the Academy next year. The year begins in January, and you have one month of downtime in december. That gives you about two months before your class begins."

"But Gramps, I wanna learn stuff now!"

"First of all Naruto, you should be happy. Most children don't join the Academy until they're seven years old. But there's plenty you can do. Since I taught you to read you can use the library to learn. Here, I'll even give you a special pass granting you access to the shinobi portion."

As the Hokage dug around in his desk for one of the different access-granting passes he had, Naruto had to suppress a smile. He had managed to get access to a massive wealth of information. It was wonderful.

Sarutobi quickly signed the card and then handed the boy the small slip of laminated cardstock, and the boy was immediately out the door, with a loud cry of "thanks Gramps" before he slammed the door.

Good luck Naruto. You'll need it.

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Naruto heaved a massive sigh as he left the Hokage tower. That had been difficult. And yet in the end, he had managed to maintain his visage of being an ignorant fool. In fact, the only reason that he had been able to pull it off at all was that he used to actually be like that.

His intentions behind acting like he did were rather simple. He was not yet sure whether or not he could trust the village. Sure, everyone he cared about lived there, but that was very few people, and everyone else treated him like shit. In fact, some of them had tried to kill him. If one of the three people he cared about were to betray him before he made some more... then he would probably turn his back on Konoha forever. But as it was, he lived and breathed for the Hokage, Ayame and Teuchi. In his eyes, everyone else was trash until proven otherwise.

Then, with a spring in his step, he set off towards the vast Konohagakure Library, pulling out his special access pass as he went.

When he got there, he showed the chuunin at the front of the Shinobi section his card and walked right through the small hardwood door. Into what was quite possibly the most beautiful thing he had ever seen.

Stretching in front of him were two rows of bookcases, one on either side. These two rows continued forward for what had to have been at least 1400 feet. Each bookcase was twenty feet wide, and there was only about five feet in between each of the two-foot thick. This continued about 90% of the way down, where all of the bookcases were replaced with racks of scrolls, all pressed tightly against each other.

In his joy, Naruto sprinted to the end, reading some of the small metal labels abundant on the edge of every bookcase. Training manuals, chakra theory, chakra control, Ninjutsu. All of it was wonderful to him.

He spent the rest of the day reading in there, flying through three full training manuals and skimming six books on chakra control.

What he learned that day surprised him. Apparently his chakra control could already be considered almost perfect. Though the books never specifically mentioned his techniques, they did make reference to elemental and shape manipulation, saying that they were both difficult to master, and incredibly powerful. They also mentioned other skills that used purely chakra—water walking, tree climbing. Both seemed like useful skills; both seemed foolishly easy to Naruto, who had practically done each one already.

Naruto spent every morning until January first in there, testing out what he learned after lunch, as well as perfecting what he already knew. By the time the December rolled around, he had already mastered his control over his "sharp" chakra, such that he could shoot his "arrows" a half-mile, and only his "poor" accuracy at any greater range kept him from going farther; his control over his "Spiraling Chakra Sphere" was such that he could form it in a second; water walking and tree climbing had proved trivial, mastered within one hour; the Clone, Body Replacement, and Transformation Techniques seemed the simplest things in the world to him.

But the Academy Three, as they were known, introduced him to a whole new idea. The idea of "General Ninja Stupidity", as he called it. It bothered him a great deal that nobody but him cared how the techniques actually worked. All that the scrolls told him to do was make the hand-sign(s), channel the chakra, say the technique name, and picture the results in his head. Furthermore, why did he even need to say the technique name or even use hand-signs? He could feel how the chakra molded, and he certainly didn't need any sort of foolish gestures or verbal components to guide his energy.

And so Naruto spent the next month studying Chakra Theory and trying to figure out how each of the Academy Three worked. The Clone and Transformation were simple to grasp the basics of. The Clone Technique forced the user's chakra into the user's own shape, creating a veritable "shell" of special chakra that mimicked the user's appearance. Essentially, by focusing on it, he forced the chakra to take on color and shape. But the significance of this was lost on most people. They only knew the hand-signs and what to picture in their head, whereas Naruto knew that he was creating a chakra construct with characteristics that he imposed his will on to create. After that, it was a simple matter to perform the technique without hand-signs and silently, and even create constructs of different shape and size. Unfortunately, they were the same as the static ball that he had created early on in his shape manipulation training—as soon as they were touched, their form was disrupted and they dissipated.

The Transformation Technique was almost identical to the Clone Technique, except instead of creating the chakra construct outside of the body, it was created around the body. This led to the small problem of a lack of physical being, so if the user Transforms into something larger than his or her physical body, the Transformation will be broken by touch, just like a normal Clone. Furthermore, if someone transforms into something smaller than themselves, they must not only create the image, but hide their own body by making light bend around it instead of bouncing off of it. This was a particularly difficult skill that most Genjutsu masters had trouble with, let alone a young boy. If not performed perfectly, the air would seem to shimmer and shift around the hidden person. Essentially, Transforming into something smaller than yourself was making a clone and turning yourself invisible at the same time. Naruto was forced to spend a week in the library studying the civilian sciences involving light in order to understand how he would do it, and he also had to spend his afternoons doing it properly.

With two weeks left until he began attending the Academy, he began his most difficult task—breaking down and understanding the Body Replacement technique, the simplest on Ninjutsu.

Naruto entered this task understanding that it would be both incredibly difficult and incredibly rewarding. He knew that the Body Replacement was not truly understood by more than a handful, because nobody had ever written it down or made it common knowledge. But he also knew that the within the well-known Body Replacement technique may lie the secrets to greater techniques, the ubiquitous Body Flicker technique as well as, and this was all too exciting to the blonde, the Flying Thunder God Technique that had made the Fourth Hokage the master ninja that he was.

What he found was exactly like what he had been expecting, though less than he had hoped. The Body Replacement was not really a replacement at all, but really just high speed movement. First, an invisible string of chakra stretched from the user's body to the object to be switched with. This led to the belief that you must be able to see what you wish to switch with. In reality, there simply needs to be nothing in between you and what you want to switch with. After contact is established, the string becomes taught. In a split second, the string contracts rapidly, flinging both the user and the object at high speeds. As they reach their intended destination, they slow down quickly, stopping when they reach where the other previously occupied.

The results saddened Naruto. Clearly, that was not anything like how the Flying Thunder God and the Body Flicker worked.

With all three of the Academy Three, there was an extra component added to the Technique—a poof of "smoke". In reality, this was really just dust gathered, condensed, and released by the chakra let off during the technique. While it was an interesting way to make use of any extra chakra that most Academy students let off by accident, it was worthless for Naruto, whose control was impeccable. Except for in the Body Replacement, then the dust was useful in concealing what direction he had moved in. So he simply got rid of that component for the other two, which consequently also got rid of the "poof" sound they made when used.

So it was on January first that Uzumaki Naruto first stepped foot within Konohagakure's Ninja Academy, prepared in advance for a rather boring four years, capable of performing all three required techniques silently, perfectly, and without hand-signs. But he also knew that he would learn things that he couldn't on his own. With the help of friends he was sure to make, he could learn to trust again and stay away from the darkness. And, with a proper training regimen, he'd be able to tone his body to become that which he would need as a ninja.

And, most of all, he'd become the best liar in the world. He couldn't let a village he couldn't trust know how strong he really was, could he?

A/N: Alright, what do you think? Please review!