Author's Notes

Well, here we are again. After reviewing the last chapter, I can safely say that I am sick of hospital drama, so I will do everything in my power to prevent similar events from happening. It was just a necessary evil to get the story going. I will say that I felt the ending of chapter 1 was weak, perhaps a bit rushed, so I may go back and edit that sometime in the future. Last chapter reached a little over 2,000 words, which is less then I had wanted, but I could not think of a way to make it to much longer without it becoming apparent that I was just dragging it on (aside from the corrections I hope to make to the end, but those would not be too long anyways). I will try to make future chapters longer, but I can not and will not promise the 6,000 word long chapters that some authors manage the roll out consistently.

Also, it will become apparent to those of you familiar with Prototype that I have altered slightly and/or built upon a number of the elements of the game. Please realize that if and when I do this, it is so that I may write a descent story.

Disclaimers were included in chapter 1, do not expect to see them again.

Chapter 2

Observations

Friday July 11th,:03am

"What have we learned?" Sarutobi asked.

He sat in his office, before him were six people. Saito, the head doctor, a nurse who had been there throughout the ordeal in the hospital, the chakra sensor Mai, as well as three ANBU who had been investigating the incident.

"About what happened to Naruto, or about how it happened?" Saito inquired.

"Both, but let us start with how it happened."

One of the ANBU stepped forward. "Sir" he saluted. "As ordered, shortly after the incident we had the area where it occurred evacuated and quarantined. Later, after everything was secure, we investigated the location of the incident, we also spoke to one Umino Iruka."

"And what did you find?"

"At the scene... nothing, sir." the ANBU replied.

"Nothing?" Sarutobi asked, a frown on his face. "Are you certain?"

"Yes sir. We tried everything, from having the Inuzuka come through with there hounds, to having highly experienced members of the Hyuuga examine the area in detail with their Byakugans. We found absolutely nothing out of the ordinary- even where we found the trace amounts of blood from his injury."

"...I see." Sarutobi spoke after several moments of silence. "And what of Iruka, what did you learn from him?"

"According to Iruka, who had been in the area shopping at the time, he observed Uzumaki running down the street in his usual manner-"

"Excessively happy and full of energy?" Sarutobi cut him off.

"..Yes, sir."

"Had to clarify."

"Yes, sir. As I was saying, Uzumaki was running down the street in his usual manner when, he apparently tripped."

"...He tripped." Sarutobi deadpanned. Could all of this have really happened because Naruto got too excited and tripped? Of course, there was the distinct possibility that whatever happened did not originate from an outside source, but still...

"Yes, sir, that is what Iruka said." the ANBU shifted. "Apparently, Uzumaki scraped his hand when he fell. I've had several other witnesses confirm this, one of whom was an off duty member of the military police. All say that after the accident, Uzumaki whined about the injury for several minutes, before standing up and, after muttering something about 'not receiving the respect he deserves', got up and began moving towards his destination which we believe was-"

"Teuchi's ramen shop. Ichiruka, was it?"

"Yes, sir. Anyways, Uzumaki continued walking for several minutes, during which time Iruka states that he finished his shopping and was about to leave for home before he noticed something was off about Naruto."

"And what did he notice?"

"Iruka reports that at first it was just Naruto's posture that was off, he had begun walking slowly and seemed almost as though he was dizzy. Iruka says that he had been going over to check up on him, when Naruto collapsed. Witnesses say he fell to the ground and seemed to be in immense physical pain when Iruka got to him. After a brief analysis, Iruka decided to take him to a hospital. Half way there Naruto is reported to have began suffering from violent shaking fits to the point where Iruka feared he was having seizures. A little ways further and he, Iruka that is, was intercepted by a jonin, who after receiving a brief explanation of the situation used shunshin to get Naruto there faster."

Sarutobi nodded. "The name of said jonin?" "Gekko Hayate, sir." the ANBU replied.

Saito frowned. "It is looking more and more likely that whatever did this came from outside his body." he said after a moment. "I still cannot understand what could possibly do something like this! I mean, the cellular death and regrowth, the changes to his physical structure, fighting off the fucking Kyuubi!"

"Well, to be fair, it wasn't fighting off a full powered Kyuubi no Kitsune, Lord of Demons." one of the other ANBU present commented. "Rather, it was fighting off a severely weakened, thoroughly sealed, former Lord of Demons."

"That's beside the point, and fighting off the Kyuubi's energies at all is still a testimony to this thing's power."

"I suppose this brings us to the next matter." Sarutobi said. He paused for a moment to take a draw from his pipe. "What do you have to report about Uzumaki Naruto's situation, Saito? You just said something about changes to his physical structure, what do you mean? And what of his memory problems?"

"Ah! Yes, you see, at first there were no apparent changes to his body, but upon further examination we found several things that were out of place." Saito paused and moved to gather some papers from the nurse. "Let's see... First of all, we found that his muscle density has increased tremendously, it has at least doubled. With this increased muscle mass, he is roughly twice as physically strong as he was before and three to four time as fast. Some of his senses have become a little sharper, specifically his vision, though his hearing has improved to a degree as well."

"How much 'improvement' are we talking about here?" Sarutobi inquired.

"His vision, like I said, is better. Not better in any particular way, mind, but simply... enhanced a little ways beyond what the normal human eye should be capable of. There is, however, one little oddity, his eye seems to now posses far more light reception cells then it should, which would serve to give him enhanced vision in the dark. Not 'like a cat's', just enhanced. The hearing is.... I would say, roughly forty to fifty percent better then an ordinary human of his age group."

"And of his physical strength and speed?"

"Well, as I said, his strength has roughly doubled- which, I should point out, is not as impressive as it sounds. Twice the strength of a seven year old is really not that amazing. And his speed has increased by a factor of four. Again, same issue as with his strength"

"I see." Sarutobi said after several moments. "And what of his memories? Are they coming back?

"Gradually, sir, yes. Naruto's memories seem to return piece by piece when we talk to him about the past, or show him familiar places, though these times when his memories return seem to always come with an intense headache, so there is a limit to the number things we can get him to remember each day. I fear we may never get all of his memories back in order, but at the very least I think we can get him back to a state where he can go through the routines of his normal life without being entirely clueless about what is happening and how to deal with it. All that said, after an explanation is given to the staff at the academy, Naruto should be perfectly fine returning."

"When will he be released?"

Saito frowned thoughtfully. ".... Possibly early next week, but no later then next Saturday."

"I see." Sarutobi spoke as he moved to write something down on a piece of paper. After he finished, he called for a courier, who entered the room swiftly, and handed the piece of paper to him.

"Deliver that to the academy administrator."

"Sir!" the courier saluted before moving to leave just as swiftly as he had arrived.

"Are there any other issues to attend to, or reports to be made?" Sarutobi asked the group before him.

"Sir." the chakra sensor, Mai, stepped forward.

"What is it, Mai? I suppose if you have something to report involving this incident, then it must be in regards the fox's chakra."

"That is correct, sir."

"And?"

"Well, sir, it's chakra has reemerged."

Sarutobi sighed. "I feared that was what you were going to say."

Mai nodded. "Sorry, sir."

Sarutobi shook his head. "And what do you have to report about it specifically?"

"It is again trying to fight off then phenomenon, though it is doing so far more... carefully this time. It is using different tactics to do so."

"What do you mean by 'different tactics'?"

"I have confirmed, with the assistance of some of the medical staff, that the Kyuubi has adapted a new approach. The Kyuubi's old tactic was basically to spread it's chakra throughout Naruto's body and try to kill as many of the changed cells as possible while replacing them with newly grown cells like the ones he had before he became host to the phenomenon. However upon seeing what that led to, namely the near death of it's host and, by proxy, itself, Kyuubi has adapted tactics which have far less collateral damage."

"The Kyuubi is concerned about collateral damage?" one of the ANBU asked, sounding amused at the idea of it.

"When to much collateral damage could lead to it's own death, yes, it is." Mai responded. "As I was saying,the fox has adapted a new trick. Now, instead of killing the changed cells indiscriminately, it seems to be trying to... suppress them. It's trying to stop them from reproducing and spreading, while at the same time, promoting the growth and spread of Naruto's old cells. Even so, the phenomenon has succeeded in spreading to more then two-thirds of Naruto's body, including his head."

"I see." Sarutobi took another draw from his pipe. "Thank you all for your assistance in shedding a little light on what has transpired with Naruto, be aware that I may call on you in the future if more complications arise, especially you, Saito. Also know that all reports regarding this are to be regarded as state secrets. Any and all reports or information on it are to go directly to me, and me only. Saito, I must inform you that I have taken the liberty of having all records regarding this incident removed from your hospital. Also know that the records that were on route to the administration buildings have been intercepted and taken.

Saito seemed surprised for a moment but quickly collected himself. "Understood, Lord Hokage."

"But...but why?" the nurse present asked sounding confused. Saito shot her a look with a very clear message. 'Do not question the Hokage.'

Sarutobi decided to indulge them a little."I do not wish for the true nature of this incident to become public knowledge because if I can play my cards right, I may be able to twist this to my, and

Naruto's, advantage. Oh, and Miss Sayoko, do not worry about contacting the other nurses who were involved in the incident. I have already had my ANBU speak to them "

The nurse, Sayoko, nodded. "U-Understood, Lord Hokage."

Sarutobi nodded. "Good." He moved back to his desk "Now, you have all made your reports?" Everyone nodded. "Excellent, now then you are all excused. I have other matters to attend to."

Monday July 21st, 8:53am

Umino Iruka sighed as he stared at the sea of annoying children before him. There were times he wondered just how it was possible for them to be this infuriating. 'Was I this bad when I was their age? Good God, it's a wonder my teachers didn't go mad and slaughter us.'

'Really, they haven't noticed that I am here yet.' He sighed. "SHUT UP YOU BRATS!!"

Silence descended over the classroom. The ones who had been talking looked like deer who had found themselves in the path of a ninjutsu. After several moments, one of the children in the back spoke. "...Um, what is it Iruka-sensei?"

Iruka groaned. "It's just, when the teacher walks into the room you are supposed to, you know, sit down and shut the hell up." Several students in the room looked nervous. "I had been standing here, in this spot, for nearly five minutes before I had to make my presence known and I can count the number of people who actually noticed I was here on one hand and not run out of fingers."

"S-Sorry, sensei." Inuzuka Kiba said weakly, looking nervous.

Iruka gave the class a look that made them shudder. "No, you aren't. Not yet, at least. But you will be. You will be very sorry when you see the extra homework you get to do because of your failure to pay attention."

The class groaned. Many shot glares at Kiba and the others who had been talking.

"Anyways, the reason I'm here slightly early today is that we have a new student today. Or rather, an old student is returning."

"Eh!? Is Naruto back?" Kiba yelled.

Iruka had an irritated expression on his face as he rubbed his head. "....What did I just tell you about talking without permission, Kiba?" Kiba paled a little "S-S-Sorry sensei! I'm really, really sorry!"

Iruka shot him a scathing look before returning his attention to the class. "But yes, Naruto is coming back today."

Whispers broke out among the class.

"Um... sensei?" Haruno Sakura spoke up.

"Yes, Sakura?"

"What... what exactly happened to Naruto? He was out for more than half a month."

"I heard there was an accident!" Ino chose this moment to prove her status as gossip queen. " That he just collapsed down by the markets!"

"Down by the markets?" Shikamaru chose to speak up. "...Isn't that the area they sealed off earlier this month?"

Whispers broke out again.

"Quiet!" Iruka yelled to the class. The whispers continued. "Quiet or even more homework!" That shut them up.

"...To answer your question, yes, there was an accident. I do not know the specific details, but I do know he was left with amnesia."

"Amnesia?" Sasuke asked in disbelief. It was rare for Sasuke to speak up, but to be fair it was rather unbelievable.

"Yes, amnesia. Which is part of why he was out for so long. He needed therapy to help him remember at least some things before he could return."

"So..." Sakura spoke up again. "Just... how much does he remember? I mean, does he remember any of us?"

"From what I understand, he vaguely remembers some of us. I do not know specifically who or how much. Also, his personality is supposed to be somewhat different, though how much, they did not specify. Anyways the point of this is that Naruto is probably going be somewhat confused and uneasy with this, so be nice and try to help him when you can."

"When will he be getting here?" Ino asked.

"He should get here some time in the next ten minutes."

It was thirty-three seconds later, almost exactly nine o'clock, when Uzumaki Naruto walked in to the classroom.

Iruka blinked. 'Right on time? And with no flashy entrance?' He mused. 'Either the Hokage managed to convince him to arrive on time and behave or... there really is going to be a noticeable change in his personality.'

Looking at the boy he actually seemed nervous. 'A really noticeable change'

Naruto stood in front of the class. After the silence continued for several moments he began shifting uncomfortably. Iruka was seriously amazed. 'Naruto is acting shy!? Unbelievable, I was told to expect some change, but this is like a different person!' Iruka guessed this was what was going through the minds of most of the children in the class as well. 'Well, maybe it's a bit early to say a he is completely different, but still...' Seeing as Naruto was looking increasingly uncomfortable, Iruka decided to break the ice.

"Class, say hello to Naruto... er, again." After several more moments of silence, the class seemed to pull itself from it's stupor and a chorus of greetings went out.

"...Um, hello." Naruto said uncertainly.

Many were having difficulty believing what they were seeing. A meek Uzumaki Naruto! Sure, he was not as bad as Hinata, nowhere near really, but to see the Uzumaki Naruto, the same boy who had earlier that same month shown the class his progress in his 'Jutsu that Would Defeat the Kages' aka Orioke no Jutsu and promised to one day paint the Hokage monument as a prank act like this had several of them thinking that the world was ending.

"...Where do I sit?" Naruto asked Iruka.

"Over there, next to Sakura." Iruka indicated to the pink haired girl.

Naruto found his way to his seat.

The day's lessons seemed to drag on. Many sat there on the edge of their seats, expecting that, with the return of Naruto, a colorful prank would come and brighten the day. By lunch it was clear to most that there were no pranks coming.

Monday July 21st , 12:03 pm

Naruto sat out in the courtyard, eating a lunch from Ichiraku's that the Hokage had been generous enough to buy for him. He wasn't quite sure he liked the academy, everyone here seemed to keep staring at him. 'Although,' he mused 'the old man did say I should expect this. I was apparently a trouble maker before my accident. If I was as bad as many seem to imply I was, then they were probably surprised to see me just sitting there.' He had tried to find it in him to start pranking, he had thought that maybe if he tried things he was supposed to have enjoyed and done often before the accident that he might get more of his memories back, but he just wasn't getting any pleasure out of it. A small part of his mind kept insisting it was just a waste of time and the rest of his mind just didn't seem to care. 'And on top of everyone staring, the lessons here are boring as dirt.' Of course that wasn't stopping him from memorizing every detail. He didn't really understand it, but ever since he awoke after the accident, every time he saw or heard something he considered even slightly important it was like a 'record' button was pushed and every little detail from what he saw to what he smelled was memorized in perfect detail. It was an odd thing, when he told the old man about it he was told that he may have photographic memory.

Naruto was also rather annoyed by the fact that there was someone following him. Yes, very annoyed. Whoever it was was not very good at staying unnoticed. He gave an irritated sigh. "Can I help you?" he asked, looking towards the corner his stalker was hiding behind. Naruto was rather surprised when three people walked out. He recognized them from class earlier as Sakura, Ino, and Kiba. "Is there any reason you have been following me?"

It was Kiba who spoke first "Hey! It isn't like I wanted to follow you around! These two" he gestured to Ino and Sakura "dragged me into it!" he shouted in indignation.

"How did you notice us?" Ino demanded in a haughty voice. She seemed to be really bothered about something since the initial embarrassment over being caught faded.

"You are not very good at hiding." he stated. Ino looked humiliated.

"This coming from the dead last!?" she returned hotly. Naruto frowned. Was he really last in the class? That was no good. 'I can hardly afford to stay so far behind.' he thought dejectedly 'I had hoped that I had good grades before the accident so that I wouldn't have to worry about doing too much extra studying to keep my grades up. So much for that thought, between the amnesia and half a month of missed class I'm going to be drowning in make up work and extra studying for all of the foreseeable future.' Naruto grimaced at the thought. Returning his attention to the group before him, it occurred to him that he could hardy let her comment go without any comeback.

"Apparently so." he said evenly. "I guess that means you really suck. I suggest taking extra classes."

Ino stared at him in complete disbelief. Kiba and Sakura joined her. They had all expected Naruto to snap at Ino's comment, he would always snap when someone called him 'dead-last, and possibly give one of his 'I'm going to become Hokage!' speeches. Instead, he turned it around on Ino and made her look like a moron.

"Now if you would excuse me," Naruto said as he got up to leave in order to avoid any more verbal sparring with Ino "I have to go speak with Iruka sensei about something."

"Wow... sensei wasn't kidding. He really is different." Kiba said after several moments of silence.

It took Naruto several minutes to track down Iruka. He found him by himself at a desk in the library. "Um... sensei?" Iruka looked up "Oh, what is it Naruto?"

"Am I really the worst student in the class?"

Iruka stared at him blankly for a few moments before sighing. "...Academically, yes, you are at the bottom of the class."

"And in field tests?"

"...You are below average there as well."

Naruto grimaced. 'Fantastic.' he thought bitterly.

"Look Naruto, I do not know who told you that you were at the bottom, but don't worry to much. It's still early in the school year after all, you should have plenty of time to catch up."

"But I've forgotten at least half of the lessons I learned before the accident!" Naruto protested.

Iruka frowned. 'Actually he skipped so often he probably could not remember those anyways,' he thought 'but still, I see his point, this could be a problem.' "And what do you want to do about this?" he asked.

"I... I was hoping that I might be able to get extra lessons to help me catch up."

Iruka stared in disbelief. Naruto was asking for extra lessons? Unbelievable. Maybe the world was ending. Shaking himself from his stupor, Iruka said "I suppose I could give you extra lessons for a while to help you catch up, but I am only allowed to do so much, Naruto."

"What do you mean?"

"There are rules. You see, while I can probably get away with giving extra lessons now because of your situation, in a month or so I will have to stop because after that, other children may start to view it as favoritism and tell their parents, who would then tell the administrators which-"

"Would get you in trouble." Naruto finished.

"Exactly. Now I can still help you after that time is up. I just will not be able to give lessons. Giving advice, recommending reading materials, and other such things are just fine, but..."

'Well,' Naruto thought to himself 'it's better then nothing.' "I'd like to take the extra lessons sensei."

Iruka nodded. Returning his attention to his desk he grabbed a piece of paper and wrote something down on it. "Meet me here at the academy every day except Sunday at six o'clock. Here." Iruka handed Naruto the note he had written "I would like for you to get all of the books on this paper from the library and begin reading them. Most of the books listed are novel length, meaning that they are around five-hundred pages or so, so you do not have to worry about reading them all to quickly. Still, I would like you to finish one book every week."

Naruto stared at him in disbelief. "I've never even read a book that long! At least, I don't think I have... But anyways, that's ridiculous! A novel each week on top of extra field lessons and class!?" That-"

"You are the one who wanted to make up for the missed work and we don't have that much time to do it in."

Naruto was noticeably unhappy.

Iruka sighed. "Look, I know I seem like a task master, but we need to get this done as fast as possible. I realize that a novel a week is a lot, but don't worry too much if you can't get that done. The novel a week goal is more of a... high target. We will aim for that, but it's not an actual limit. I won't get mad if you fail to hit that target, but I will be quizzing you every so often to make sure you are reading the books."

Naruto demeanor improved a little, but he still looked put out. He sighed. "I understand."

"Good. I expect to see you after class today."

Naruto nodded and left. 'Well' Iruka mused 'things are going to be very different now. I wonder how things will change.?'

Author's Notes

Well, this is chapter 2. I can say I am happier with this one then I was with the first, both because it is longer (nearly 4,200 words not counting author's notes) and... just because? I dunno. Anyways, these first two chapters were pretty much prologue chapters before the actual story. They served the purpose of giving insight into what happened and providing an idea of why things will have changed after the time-skip (which will have occurred between this chapter and the next one and will jump to the end of the academy years, right around where the series started)

I know a lot of you, after reading the description of how Naruto has changed are going 'What the fuck? That's it?'. Realize that there are major differences between Naruto's situation and Alex's. Alex was in danger constantly after awakening, which probably played no small part in causing him to change as quickly as he did, and would routinely devour people after he figured out how which was stated to make him stronger and smarter for each person he devoured. Naruto... has not consumed anyone. And he would probably have problems with that act. Keep in mind that I am not trying to make a completely OOC Naruto, I am basing the 'Naruto' I am using off of canon and am trying to keep changes to his personality realistic based on what happens to him and things that change (granted, you do not yet know all of what has changed/happened, but it would be spoiling to tell you).

Too put it bluntly, Alex Mercer was a bastard. A Magnificent Bastard, yes, but a bastard none the less. He had no problems consuming people because he apparently got a phd in 'not giving a fuck' along with his diploma in genetics. The number of people he cared about could literally be counted on one hand. Naruto on the other hand, cares about people. Not just people he knows, but complete strangers too. Even ones who harm him and people he cares about. I feel the act of consuming people and stealing their memories and skills would have a dangerous psychological impact on Naruto (though this certainly doesn't mean I am going to be ignoring that little trick).

Also, keep in mind that the Kyuubi is there fighting Blacklight every step of the way, doing everything in it's power to stop and hinder it. This is not helping Naruto gain the advantages of Blacklight related changes at all.

In short, bear with me here. As I had said at the end of the introduction in chapter 1, all will become clear with time.