Disclaimer- I do not own Naruto in any way or form.

Chapter 1- Only a Shell Remains

Song- Bring Me to Life

A great demon attacked the Leaf Village, killing many, and taking their hero, the Fourth Hokage. A hero's wish for his son to be left in peace never was put into force. Thus the boy was left to fend for himself.

Upon defeating the Fox, the people that were expected to watch the boy dwindled,.

Jariya

Tsunade

Kakashi

Sarutobi

Each expected the other to do their duty, but their lack of care would bring upon them doom.

This is the story of Naruto Uzumaki.

(Nearly Six Years Later) Somewhere in the Leaf Village

Rapid footsteps we heard echoing throughout the village of Kohona. Civilians closed down heir shops, locked their doors, blinded their windows and blissfully ignored what was about to happen in their very own village. Ignored the barbaric acts that would occur, as they did in the past.

From an alley way appeared a small boy, no older than five years old, breathing heavily, sweating profusely, eyes wide with a fear that no child should ever experience.

This boy was Naruto Uzumaki, the container of the Nine Tailed beast that took away the village's hero, the Fourth Hokage. For this the people saw no other choice but to hold him accountable for their loss. And so this is how the story of young boy aspiring to be Hokage can change so very easily.

Turning behind him the young boy saw the fire from the torches of his chasers. Pushing his body to continue he resumed running trying to find place that could be safe from them, something that he tried to do nearly everyday but when people thought of you as a demon it was quite difficult; a lesson that young Uzumaki quickly learned.

He was running so blindly that he didn't even see a person right ahead of him. Running into the person had knocked him onto his back.

Straightening out and clampering to his feet he stammered out an apology, "Sorry for running into you," looking at the person he gulped; the man stood at 6 feet tall towering over him, "Gomen."

Smirking evilly the man started to reach his hand out the boy, "Don't worry I'm sure that we can work something out." His other hand came from behind his back revealing a knife.

Eyes wide with fear Naruto ducked under the man's hand and ran between his legs to escape. "Get back here demon. Everyone he's this way, come on."

With that thought in mind Naruto tried even harder to avoid the crowd following him but when his path lead to a dead end he stared dismally at the stone wall before him. Looking back to see if he could escape his heart dropped when he saw that the crowd was at the entrance.

"Looks like you're trapped demon," backing into the wall Naruto closed his eyes shut as he waited or the inevitable to happen, "Oh no you don't demon, you're going to feel everything that we do to you, you will never forget this night, just as we never forgot when you attacked us."

A cheer broke through the crowd as person after person took their turn, kicking, beating, burning, stabbing the boy. Each one with no sense of mercy; no sense of remorse.

The pain came, pain so unbearable he screamed to the high heavens for help, he screamed for anyone to come help, he prayed for a hero to emerge from the dark and save him just as the stories he read; but no one came, no one tried to stop it, all over the village his screams were heard but no one came.

A little boy's hope was crushed that night, his innocence robbed (NOT HIS VIRGINITY), what could have been a boy that would rise into a hero would never become, now only a shell of this self remained.

In the resident Hospital Emergency Care Unit

"Naruto are you feeling okay?" The young boy just continued to stare straight ahead, "Please Naruto you have to answer me."

Moving his head slightly to the side he answered in a small voice, "I'm fine"

Taking another look at the boy the Hokage rose from his seat, "I must talk to your doctors and nurses so please excuse me for a moment." Exiting through the door the old aging man took several deep breaths.

"What happened to him? What is the damage?" Looking at the nurse and doctor in his company he braced himself for the results.

Taking a few moments the doctor give the list of injuries, "He suffered from a broken leg, both broken ankles, 6 broken ribs, internal bleeding, a nearly shattered pelvis, each finger was broken along with his wrists and both arms, his shoulder was dislocated, broken nose, jawbone, and a severe cession. His eyes were swollen shut and his ear nearly cut off. There were third and second degree burns all over his body. It s beyond a miracle that he managed to survive Hokage-sama"

Taking another breath he asked, "Is that everything doctor?" He started to move as he thought nothing else can be worst than that, how wrong he was.

"Um no sir. There is still one more thing that you should know," Tuning to the doctor he nodded for him to continue, "His vitals and brain wave activities show something else. He was awake and aware of all of these things happening to his."

The Hokage stood in shock as his hat dropped to the ground. For a child to experience that while being aware of it all was most disturbing. 'Minato you must be rolling around in your grave at such treachery'

"Thank you Shiro, you have done a great job helping him."

"It is my duty sir." Bowing slightly he added, "I have other patients that I must get to, by your leave sir"

"Oh yes of course you are dismissed."

Going back into the room accompanied with the nurse he looked at Naruto. His heart sank as he realized that he had failed him, he failed his parents.

"Well Naruto the doctors say that you can leave within a few days o that will be good." Not getting any reaction from the boy he continued on, "When you get out I will even treat you to some lunch how about ramen?" The boy always got excited about the delicious noodles but it sparked no reaction at the present.

"Why did they do this to me? Why is it always me?" Without turning around the boy seemed to plead for answers.

"Naruto I want you to know that I am so sorry for what happened to you" Still no reply he gave a weary sigh, "I must return to my office but I will check on you later okay."

Taking one last look at Naruto he bid his goodbye.

Now only the nurse and Naruto remained.

"You know Naruto it is amazing that you can heal so fast I can only heal little wounds fast. Would you like for me to show you?"

Looking at the man, he figured that anyone who can heal cant hurt him, he nodded his head nervously, "Yes please sir".

Focusing his chakra on the boy's cut hand he healed it.

Sparking a small smile from the boy "Cool."

"Yes it is very cool Naruto would you like to learn some of it?" Looking at the nurse who had taken care of him he nodded his head. He would trust this man for he did help save his life.

"Good. By the way my name is Kabuto, Naruto-kun. Pleasure to meet you."

Hokage's Tower, Hokage's Office

"Why was the boy wandering on the streets so late at night Hokage-sama? You should know how dangerous it is for the boy." The Hokage took deep breathes as it was taking everything in him not to pull his own hair out.

"The place in which he was staying at kicked him out so he had no choice."

"Well then why would you place him with those people?"

"I thought they could be trusted."

"Well then we both know what to think of your judgment."

Glaring at the man before him he posed the question that had been at the back of his mind every since he entered the room, "What is your concern with the boy, Danzno?"

Looking slightly afar, "He is the jailor to the most powerful being on the earth, it is imperative that he be kept alive for al of our sakes." Turning to the most powerful man in the village he continued, "But apparently not everyone thinks that way."

"Are you implying that I do not care for the boy? I remind you to mind your tongue." Leaking some of his killing intent at the crippled man for suggesting such a thing.

"Of course not Hokage-sama, I was only saying that there are other people that do not share out concern for the boy."

Leaning back in his chair the Hokage took a deep puff from his pipe, "There is nothing that we can do about the people's opinion of him, what is done is done, we must only hope that the best outcome results from the situation."

"You would sit by and watch as a child is abused, the child of the greatest Hokage this village has ever seen?" Snapping his eyes to Danzno he was surprised "You know of his heritage? How?"

"It is easy by taking just one look at him. Don't take me as a fool."

Looking out the window he resumed his previous thoughts, "There is still nothing that I can do about that"

"How the power of the Hokage has fallen, I will take my leave now Hokage."

Without looking to see the glare that the Hokage was throwing at his back he tuned to the door."

Exiting the office Danzno tried to collect his thoughts to form a plan to use these new turn of events in his favor.

'The boy would be a force to be reckoned with when he got older, his parents being very proof of that as well as what is sealed into him will be factored in. If he could only train the boy, it would have perfect results. But…

That damn Hokage won't allow anyone to train him. But perhaps I can use this in my favor.

The boy is obviously hurt by the Hokage's lack to do anything; if one more thing were to push him over the edge he would be much more willing to be rebellious. But what could set the trigger…'

His one eye widen as he thought of it, the boy's heritage. 'If the boy knew that the Hokage willingly withheld that information from him he would be furious.

Still was it a risk that was worth taking, the boy was still young and impressionable, that could work in my favor though.'

It was decided, 'I will try to recruit the boy. Perhaps not for Ne right off the bat, bt later when he has grown to trust me more.'

Smirking he gave himself a small pat on the back for the ingenious plan. With all his thoughts focused on the plan he barely realized that he was already home 'Well Sarutobi your care for the boy will give me the opportunity to train him for Leaf's will. I must thank you some time.'

Hospital, Naruto's Room

"Well Naruto-kun I would not have expected you to be able to do the justsu on your first try it is extremely difficult and requires years of studying in order for it to be used correctly" Smiling he gave Naruto a warm look while he continued to file some paper work.

After giving the justsu one last try he turned to Kabuto, "What is the use of being able to use this, you said that I have a very good healing system so it wouldn't really benefit me all that much"

Giving the boy a look of surprise, 'To think that a young boy his age is able to have this level of deduction and awareness, incredible.' "Well you can use medical justsu for ore than just healing"

Seeing his confused look Kabuto reached into his bag and retrieved a book on the basics of fighting with medical justsu something that he himself excelled at. Handing it to Naruto he said, "Read this, it might help you while I finish this paper work."

Truth be told he was already finished with it, he was just giving the boy time to read the book, and to give him a chance to work with this finding.

'The boy is hated by the village, has potential to become a great shinobi, and from what I can tell has a thirst of knowledge.

Should I try and give him to my master Orocumaru?

Should I teach him and have him indebted to me?

Choices. Choices.

Or…'

Smirking to himself ' I could just teach the boy and leave it at that. Kami knows that spies only turn to betray their masters if I am any proof of that. Bt if I teach the boy he will naturally feel indebted to me and that would just be icing on the cake'

Glancing again at the boy he outweighed the situations, ' The Hokage cant get mad for him learning some medical justsu, however teaching', looking at the boy struggle to understand the words was pitiful, ' still it will be more than worth it.'

"You know Naruto I would be more than willing to teach you some of the things that I know" Snapping his had up from the book he looked into Kabuto's eyes "Really? But why?

"Well Naruto it is very lonely here in the hospital with nothing to do and most people don't even appreciate the fine work that medical justsus do so it would be a pleasure to pass on some of my knowledge to you"

Staring intently at him for a few moments he cracked a small smile, "When can we start?"

Smiling he re-adjusted his glasses 'Perfect, like taking candy from a baby. I hope for your sake Naruto that you are willing to work hard for this'.

"Well then lets just go over some basics like the smallest thing; a cell. What many people don't know is that".

Back at the Hokage Tower

Taking a deep sigh Sarutobi thought about what Naruto parents would think of him if the saw him now. Was he making the right moves, was he too stict with the boy?

'For one thing I know that they will not be pleased with me for some of the thing that have happened to him

But it isn't you fault the council goes against your every move to try and help the boy.

But I know that I could try harder.'

His argument drifted to his thoughts about Jariya. 'Last I heard from him he was taking the news of his students death hard, he hasn't been in the village since Minato's funeral, he was barely able to look at the boy that he was named godfather to.'

But who could really blame him, Minato was like a son to him, he taught him everything that he knew and then all of a sudden when a raging demon attacks you lose the closest person to you since 'Probably since Tsunade'.

Both his students seem to have grown rebellious and stopped returning his pleas for them to come home. Walking over to the picture of Minato h truly considered telling Naruto all about his heritage, about how much his parents would have loved him, but that would involve telling him that there was a person meant to take care of him who never did; it would simply crush the boy.

Taking his eyes off the picture he decided to leave things as they were. Naruto simply could not know the truth of his lineage. The cons outweigh the pros, he couldn't take time to make sure that 1 child was protected more than all others, his duty as Hokage forbade him.

Signaling the ANBU he inquired, "What do you have to report?"

"Sir we were not able to make any arrests, there were no witnesses and no one is coming forward. Sorry Hokage-sama"

THUD. His fist indented into his desk, "Kakashi how are we suppose to take care of him, how are we suppose to allow him to continue to trust us if this is the way we handle the crimes done to him."

Bowing his head the ninja with a dog mask on could do nothing, could respond with nothing.

"Are there any people that would be willing to watch over him? This madness simply cannot continue."

"No Kakashi there is no one willing to step forward. You are dismissed"

Leaving the room Kakashi felt for the kid he really did but there was nothing that he could do for him as he was in ANBU. Besides he didn't feel as though he owed the kid anything. He needed to focus his time on protecting the villages that his sensei loved so much as well as Obito's legacy.

There was simply nothing he could do. He would soon regret his lack of action as it would play a part in the ominous future.

Hospital, Naruto's Room

Walking toward Naruto's room Danzo thought about how the boy might take the news that he would be hearing. It would forever change the boy's world, his point of view on this pathetic village, and most importantly lead him down a path that Sarutobi would surely not like.

Pausing at the door he allowed the young nurse to exit, Kabuto if he wasn't mistaken.

"Ah, Danzo-san it is a pleasure to meet you" Kabuto gave a formal bow before departing down the hallway. Preparing himself for what he would be doing to this boy.

Walking into the room he noticed Naruto reading a book on medical 101. 'Hm the boy is already showing a thirst for power, excellent'

Naruto looked up from his book upon noticing someone else was in the room with him.

"Hello," closing the book and putting it away Naruto studied the man closer. He had his arm in a bandage and his 1 eye seemed to have been damaged if the bands around it were any indication, "What do you want?" Spoken with some boldness as he knew that in a hospital even the uncaring doctors wouldn't allow for there to be any fights within their walls.

"My name is Danzno, Naruto. I am one of the advisors to the Hokage." Sitting down in the chair that was across from the small boy. "I wanted to talk to you about something that might interest you greatly."

Giving the man no small amount of suspicions he voiced his thoughts, "What is it that you think that I would like and why would you offer anything to me?" Sitting up he stared intently at the man waiting fo ran answer.

"Well I don't know if you know this about me, but I used to be a ninja before I was handicapped," Turning to look at the boy he got no looks of pity 'Good', "But still even to this day I still try and pass on my knowledge of the shinobi skills down to others so that they might know how to…. Properly protect this village. Are you following me so far Naruto?"

Nodding his head Naruto raised another question, "But why would you want to train me, I am not from a clan of ninja so I might not be able to learn the things that you would be teaching me."

Smirking ever so slightly, 'Gotcha'.

"Well you see Naruto I know that you would prove to be an excellent student as well as an excellent shinobi due to who your parents were."

With that sentence Naruto snapped his eyes onto the man and gave a surprised look, "You knew my parents?"

"Yes of course Naruto, they were not my best of friends but they were excellent ninja in every aspect of the word."

Hesitantly Naruto asked, "Can you maybe tell me about them?" The look in his eyes were pleading.

Sifting his gaze out the window the recalled all thoughts of the boy's mother as that would e best to explain first. "You're mother was one of the most beautiful women to grace this planet. She was born a fighter and she died one. She was from the Uzumaki Clan in Whirlpool but after it was destroyed she came to Leaf. She fell in love with your father and they planned to marry." Looking back at Naruto he continued taking in the boy's unshed tears, "She was most excellent with a sword, her taijustsu was excellent and when she was angry even the best of ninja were wary to fight her.

"She had long red hair and the most caring personality that I have ever seen."

Taking a moment for Naruto to take it all in he observed the boy. His eyes were filled with unshed tears, a remarkable feat considering what he was just told.

"What about my father, you knew him to as well right?"

Taking a deep breath he continued, "Your father, Naruto, was the most powerful person I have ever known. He could do the most amazing things with the most basic justsu, and had a great mind. Hi leadership skills were second to none. He was undefeated on the battle field. He loved both you and your mother very much."

"What were their names?"

"Your mother was Kunshia Uzumaki. And your father, was Minato Kamikaze, the Fourth Hokage."

Steeling himself for the boy's reactions, "My father was the Fourth? B-b-but how? How is that even possible?"

"It does make sense Naruto. Your mother died while giving birth to you, and on the same night your father died protecting you and the village. They died doing the thing the loved, protecting others."

"But if what you are saying is true, then why did no one ever tell me? The son of a Hokage would have known who his parents were."

"While that is true Naruto, the Third believed that you would be best protected if you did not know. Your father had many enemies that would have come for you."

The boy was obviously not going to take that sitting down, "But why wouldn't my life have been better, wouldn't people respect me, wouldn't I have someone who loved me?" The last part was said in tiny whisper.

"Naruto you say this but you know that those emotions would be false. They wouldn't love you for you, but for your father, not respect you but only your blood."

A look of fury came upon Naruto, "Hokage-sama, he would have to have known about this why wouldn't he tell me?"

"He thought that I would be better. Naruto I do not claim to know you or what you are thinking but I will tell you this; If you were to grow strong they would have no choice but to acknowledge who you are and the power that you hold, I can help you become stronger."

Looking at Danzno he contemplated. 'if what he is saying is right then it would be in my benefit to train hard to be the best'

Stopping Naruto from answer Danzno spoke, "Don't give me a reply now, just think on it. I will be back later."

Getting up he went to leave the room but three words made him pause, "Thank you Danzno."

With a smirk he left the room, 'Game, set, match you lose Sarutobi'

Same Setting

Naruto sat in his bed staring at his hands, he the boy who was alyways beaten and spat upon was the son of a Hokage.

He may not have been the smartest person, nor the genius that others were but even he knew that there was something else that neither the Hokage or this new man Danzno were telling him. There was always a dark side to people no matter how sweet they might appear.

He had thought the old man was an exception to this rule but he was obviously fooled.

A mistake that he would never make again.

With that in mind he thought about this new character, Danzno. The man was offering to teach him his own techniques; there must be a price that he wanted Naruto to pay. Nothing in life came for free.

But the chance to train and become stronger, to become what his parents would want of him; to become a shinobi.

He truly did not want to accept Danzno's offer for training knowing that there would be some type of consequence but… 'He's giving me a chance of a life time, I cant refuse it.'

Naruto remembered a book that the Hokage gave him. It was back when Naruto didn't know about morals and that there was always something that you can get out of every story.

'I just hope that what I will be getting out of this will out weigh the negatives. Sorry old man, but he gave me something that I always wanted to know. And to now that you wouldn't tell me, it hurts more than anything else in the world. I trusted you and now I find that you've betrayed me in a way that I never thought was possible.

And for this I will never be able to fully trust you, and I will never forgive you.'

For the second time that night a boy's innocence was taken and hi faith destroyed.

Later on that night

Naruto was reading the book that Kabuto gave him. So far it was very complicated to understand.

He might be a little advanced for his age but that didn't mean that he knew what a septum meant. But really, What the fuck was a septum???

Holding his head he decided that he had enough for today. 'Kauto won't be disappointed I at least got through the first chapter. What really scares me is that this is the intro to biology. Not even the complex stuff.'

Pushing the book off the bed he turned over in the bed and tried to get some sleep, it ad been a very long day.

He was drifting off.

"Naruto, we are so proud of you"

Looking around Naruto tried to figure out where the voice was coming from, "Who is there?"

"Just know my son that we will always be proud of you. We love you so much."

"Mom? Dad?"

Snapping up from his bed Naruto wondered, 'What the hell is going on?'

A/N

New story please review. Major changes as you can see. Will try to update in a few days.

There might be some errors in the story if there is anyone that can help me with that I would greatly appreciate it.

Coming up: Talks with Sarutobi, and the beginnings of change.