Summary: Because of something he isn't, Naruto is forsaken by the Village; Left only to become the scapegoat of their pain, his unreasonable suffering is the consequence. In time, Naruto is forced away from the village and comes upon a truth regarding his heritage, that will shake the foundations of the Nations. Eventual Harem. Seal Master. Smart/Strong Naruto. Slow Pace. Read A/N for more

A/N: I will first clarify a few things, and preframe what the story will entail. A few members of the Harem have already been decided, and they are all out of Konoha, which I intend to keep. I may make an exception later down the line for one girl in Konoha, but that is an option for much, much later on in the story. Though I do have it tagged as a harem, it won't appear until later on in the story, so bare with me. I also won't mention who is in the harem until later in the story. I don't like to have things set in stone to early, I'm pretty fickle about my characters.

In this story:

Naruto is not Minato and Kushina's son, but is still orphaned

This is a MAJOR plot point for the story, that will be explained much much later.

I will not focus on Angst much, and this will be a neutral Naruto story

This means there will be light, and dark moments regarding him, but by no means is he evil, just apathetic at times.

Pacing will be slow to develop setting and characters

I take my time, so just bear with me please

Story will follow Canon for the most part

The story will follow Canon timeline at some point, but it will be going into detail more about events that took place in the background (Kirigakure war, Uchiha massacre, akatsuki formation, etc.) than the actual canon events.

Oh Lemons!

Please don't expect any lemons in the story, I have it tagged as 'M' just in case I change my mind later down the line. There may be gore and violence, as well as swearing, so be prepared for that.

Character ages do change

I should also mention that character ages may change to fit the format of my story, so as Scar from the Lion King would say, "Be Pre-PARED!"

What there won't be:

Yaoi: I am a straight male. While I have nothing against homosexual relations, I won't write about them. A part of writing is trying to imagine yourself in the characters shoes. For yaoi characters? I simply can't imagine myself having relations with a man.

NTR (netorare): Not happening. It just isn't. I dislike the genre, therefore I won't write it. You can't write something you don't like afterall. In case you don't know what this is, it is basically another male character stealing away a love interest of the main character, which in this case would be Naruto.

Rape: I may have elements in the story that mention it, but by no means will I be going into detail about it. It's not the kind of story I'm trying to make this one out to be.

Disclaimer: I do not own the Naruto Franchise or any of its characters, I am but a simple man, with a simple desire to write a fanfiction that has been plaguing my mind.

The only thing I own in this story are my theories on sealing techniques, original characters (if I decide to make any), and scenarios that did not exist in the Naruto Franchise.

Prologue

Under the dawning sun, the sounds of waves crashing and receding along the coast was all that could be heard. Infesting the air was the scent of salt and sea, tinged with a slight smell of blood and steel. For miles, all that could be seen was ocean and sand, of course, that is only the case if you ignored the new arrival, and sole inhabitant, to the unknown island.

This individual was a young boy of 8 years, who was dyed in blood and covered in sand, which burrowed into the wide array of open wounds he wore. He was dressed in an outfit that many would deem was unexpected and strange for one his age, as he was garbed in traditional ANBU fashion with a grey flak jacket and fitted black clothing with tape wrapped around his right leg. His porcelain mask seemed to have been lost in the journey to the island, as can be seen by his fetching appearance.

His muscle structure was well-defined for someone his age, and he possessed quite the athletic appearance. He was well defined all around, yet it was not overwhelming in mass. It seemed to be a fitting combination of strength and flexibility to allow perfect synchronization between power, speed, and maneuverability. One could say he was bred for combat.

His facial structure was fairly mature for his age as there was little fat to be seen, though it was a curious sight to see three scar marks mar both of his cheeks. Though they appeared evenly spaced, and adorably placed, as some females may consider it to be, it could be seen that he was indeed not born with these scars.

His hair was a sight that stayed true to the bloodline of his clan. As is genetic for most Uzumaki, his hair was a deep red that, if not distraught from his current situation, would very tantalizing and hypnotic to behold. His hair was a spiky mess that seemed to point in no particular direction and framed over his forehead. It was a wild look that would be sure to garnish attention from the female populace in the future.

His frame began to shudder and shiver as he slowly awoke from his state of unconsciousness. He coughed out whatever water he may have swallowed since his…unfortunate, situation. He struggled for air as he proceeded to vomit out a mix of water, sand, and blood. This process continued for a few moments until he was only dry heaving. His breaths started to slow, though still very uneven. As his eyes opened, you could see eyes more deep and blue than the ocean he seemed to appear from. It was catching and mesmerizing, if not for the dull light that it projected. Through his eyes, a void of emotions could be seen, with only the slightest hints of pain showing. The dullness in his eyes showed just how empty he has become.

This young boy's name was Naruto Uzumaki.

As he slowly sat up, ignoring the pain that seemed to be screaming at him as he moved his body, he glanced at his surrounding to calmly ascertain his situation. As he focused his eyes on the area around him, only three words came to mind, all of similar meaning:

Barren, empty, desolate.

These words can be used to describe the current state of this island. As far as his eyes can see, buildings were in ruins, forestry was torn asunder, and bones were shattered and spread throughout the huge expanse of his vision. As he took in his surroundings, only one place came to mind, as he whispered out in a low voice between breaths, barely audible to even himself.

"Uzushio…gakure."

As one from the Uzumaki clan, he naturally knew of his heritage, though it was only the most basic of information, as well as some tales and legends of their past. He was aware that his clan members were especially gifted in the sealing arts and possessed a very powerful life force, allowing them to live longer than the average human, though that was the limit to his knowledge. All their history, techniques, and treasures were lost since the time of their downfall. The island was guarded by the large whirlpools that seemed to protect the island, and the weather itself seemed to alter as a defense mechanism to intruders by creating tornados and hurricanes.

It was a mystery as to what the Uzumaki were truly capable of. It drove some of the great shinobi villages to hunt down their treasure even more, but alas, the power of nature proved to be a much too difficult task for the shinobi of foreign nations. It was rumored that only an Uzumaki was capable of setting foot on the island, though that still left one to wonder how it was possible and what should be done to gain entry.

Perhaps…I wasn't viewed as an intruder because my bloodline was detected? Thought the boy. It may seem strange that a child his age could be so calm depsite his current state of distress, but to him, this only seemed to be a normal thing, which lead him to reminisce what started this mess.

- Flashback-

3 years ago

The room was dark, dreary, and the only source of light being shone was upon two figures within the large room, one larger and one smaller. Following the figures in the shadows were a large number of individuals bearing ANBU masks, all kneeling in deference to the taller figure.

Naruto can also be seen kneeling before the taller figure, who was garbed in bandages that covered his right eye. He wore a dark grey robe that feel over his right shoulder, only exposing his white shirt underneath as he held his cane in his left hand. His figure was imposing and domineering, as well as intimidating. One could see a man that has been torn and corrupted by war, with only his injuries and cross-shaped scar on his chin to show for it. This is the man who had raised Naruto since he even became aware of his surroundings and was the shadow of the leaf: Danzo Shimura.

He looked down at one of his greatest prospects. A ninja he had trained from his youth, an orphan that was born during a time of bloodshed, and one of the few remaining members of a once powerful clan before its demise. He was raised to be a tool, a weapon for the leaf. But…as with all tools and weapons, things needed to be replaced. Danzo was never a man to form attachments, nor will he ever begin to do so, as he believed it was a sign of weakness. In times of war, sacrifices are necessary if it is for the greater good, and he deemed this child's sacrifice was for the greater good of Konoha.

It was barely a week since Konohagakure suffered great casualties from a tragedy that came in the form of a giant fox. The situation within Konoha was chaos with the loss of one of their greatest shinobi: Hiruzen Sarutobi.

The news greatly affected all of the citizens and shinobi. He gave his life to seal the Kyuubi into the daughter of the fourth hokage, Minato Namikaze, and the red hot-blooded habanero of Konoha, Kushina Uzumaki. While Minato originally intended to seal the fox himself, he was reminded by Hiruzen that as fourth hokage, he has a duty to protect Konoha reaches further than simply giving his life to protect them. He must protect and lead the next generation of shinobi, and lead them down the correct path while instilling them the teachings of the "Will of Fire".

Hiruzen, knowing his time as a shinobi had died down with the previous war and instatement of the new hokage, he was determined to perform the sealing himself, even at the cost of his life. His generation was nearing it's end, and believed that with his death, a new age would begin. One of greater peace and prosperity.

The whole of Konoha mourned the loss of one of their greatest heroes, along with the all the others that had lost their life in such a tragedy. However, there was a new worry that plagued the hearts of all the inhabitants of Konoha. Despite the lack of knowledge in the shinobi arts, the civilians were able to pick out the difference in how the Kyuubi was "sealed" and not killed. This was the cause of the current chaos and disparity in the village hidden in the leaves.

Where is the Nine tailed Fox? What is going to happen to the village? What is going to stop the demon from appearing again? What if the fox seeks out revenge? These questions and more became a common worry for the village, and they sought out answers.

Minato and Kushina were at a loss at what to do. They both have a responsibility to tell the truth to the whole of the village, but they were also aware of the burden that came with being a Jinchuriki. Even if their child, Mito Uzumaki-Namikaze was the child of the fourth hokage, it did not mean that she would be excused of harassment, abuse, or segregation. It was different from the times Kushina or Mito possessed the fox. The fox was safely kept away and there was no tragedy as a result. With this recent incident, there was a possibilty that there may be some individuals who will seek the death of their child through legal means…or through other methods.

That is when Danzo brought them an answer in the form of Naruto Uzumaki, and that is what marks the beginning to Naruto's current state.

As morbid and cruel as it may seem, Konoha needed a scapegoat. It needed something to ease the fear that constantly tortured their hearts and thoughts. And that is what Danzo presented Minato and Kushina.

It was known by the populace of the older generation of shinobi, that only an Uzumaki was capable of bearing the amount of chakra the fox possessed and live. How fortunate it was that Danzo had an Uzumaki in his organization he had…picked up years before. And all he had asked the Hokage for in return was the reinstatement of 'Root', and the true bearer of the fox to never be revealed to anyone outside of the ones who already knew, meaning Jaraiya, the advisors Homura and Koharu, and themselves.

They were reluctant to force another child to bear a responsibility that was never his, and furious at the suggestion as well. This was especially the case with Kushina. The Uzumaki were originally a clan of Uzushiogakure, and they never believed in the "Will of Fire" the same way Konoha did. They had a belief called the "Will of Water". Water was freeform and malleable, flexible in form and capable of changing states, yet even as it changed, it was always still water. In other words, they believed in change, freedom, and the individuality of the Uzumaki, but also believed that change was only possible as one. They were a family, an entity capable of doing so much more when together. Hence, they were water.

Her beliefs did skew more in favor of the "Will of Fire" since she spent most of her life in Konoha, but that did not mean she didn't understand her people and their beliefs. Whoever this boy was, he possessed the same bloodline she possessed, a survivor of her clan's genocide, so her reluctancy was clear.

In Minato's case, he simply did not believe any child should bear such a burden. However…if he does not go through with this, it will be his child that would bear such a burden. It was a cruel thought, but if he had to pick one over the other…it would be a fact he would defend his loved one over a stranger. This thought process of his only served to agonize him more due to the morals he had grown up with, and he couldn't help but hate how he thought the way he did.

In their conflict…Danzo fed them lies of what could come to their child. He played the strings of their emotions like a harp, gently swaying them to his proposition. It may not seem possible for ninja as powerful as Minato, and as stubborn and hot tempered like Kushina, but everyone has a weakness. In this case, their daughter Mito was a great one. They did not want their daughter to be engulfed in a future of torment and segregations. They did not want her to hear the whispered words of "Demon" time and time again. They did not wanted her to receive the constant threats towards her life, and live one where she is a constant target of assassination day to day, simply for carrying the demon who brought disaster to their village. Just because they knew the difference, didn't mean the whole of Konoha would accept it. They are in a state where they are blinded by fury and depression, and are willing to make anything a target for their negativity.

It is sad knowing how low humans will fall to relieve their own pain and suffering, while ignoring the state of others. It was a harsh truth, but a reality that can only be accepted.

Mito was a newborn, a pure and innocent life. One of which…they did not want to sacrifice. Danzo had assured them that his operative that would be replacing Mito had undergone his "training". That he was nothing more than an emotionless husk, a tool to be used as he pleased. That the replacement would receive this task like he would any other mission.

The two were appalled by his words. They were very much aware of how 'Root' was trained. And though they did not except such methods…they were slightly relieved the child at least wont suffer the negative emotions that come with bearing such a burden.

Through much deliberation and contemplation, they agreed to reinstate 'Root', only if their conditions were met. New operatives must go through the approval of the Hokage, and their training will no longer follow the same course they had experienced before. Creating emotionless husks of a soldier was immoral and not for the good of Konohas future. All missions would also need to be screened by the Hokage himself before approval. Begrudgingly, Danzo had accepted the terms…though it didn't mean he would follow it to the letter.

Which brings us back to the situation Naruto and Danzo were currently in.

Naruto can currently be seen kneeling before Danzo, one fist to the floor, the other arm resting upon his knee with his head bowed down. A sign of deference to ones superior officer.

Danzo looked upon his greatest prospect, that has now become his greatest opportunity for the revival of 'Root'.

"Raise your head, Maelstrom."

Hearing those words, Naruto slowly rose his head, revealing a porcelain mask of simple design. It was a white mask with holes for his eyes, and a blue symbol of the Uzumaki clan that stretched across. He stared at the man that had raised him from his youth…with nothing but contempt. He tempered himself however, and reigned this contempt in before anything could be sensed. If there was anything he would thank this man for, it would be the ability to control his emotions and his current strength. He could have done without the repeated physical torture and mind breaking torment he needed to experience, but he supposed his options were heavily limited. Well, more like he didn't have any other options.

Danzo truly believed he had broken Naruto's will, made him a perfect soldier, despite the fact he had yet to undergo the final ritual in becoming a 'Root', he figured it wasn't necessary seeing as his role would be changed soon enough.

Danzo, however, underestimated the will of the young Uzumaki. Their clan was known for being stubborn, as well as their…temper. At times, it was a great weakness. One that governed their actions without much thought. At other times, it was their greatest strength. Granting them power to overcome all obstacles that may stand in their way despite the odds. This was shown when they were invaded by foreign powers, and despite their loss, they did not cave so easily, taking out a large number of forces, to the point where the Third Shinobi World War that was originally planned to happen then, stalled for a period of time to regroup forces.

Naruto was a true Uzumaki in that respect. He was stubborn and at first resisted Danzo's "treatment". In time, Naruto submitted to Danzo, not out of fear, but necessity. He became aware of how powerless he was. He understood that he was incapable of doing anything at this point. So, he submitted. He understood that Danzo, while cruel, knew how to grant power. And that was what he did.

He transformed Naruto into a soldier with great potential. Despite his youth, he was capable of taking on skilled Genin, and even low-level Chunin with pure skill and jutsu. He was mature beyond his age due to his training. It forced his mind to accelerate and adapt to the changes, and the harsh reality of the world. He had started killing animals at the age of 4, and had even killed his first man at the age of five. His mind was slowly being tempered to that of a trained killer.

He was skilled in the sword, as it was another trait of the Uzumaki. Their body was highly resistant to harm in comparison to other clans, and were very flexible as well. Their extended ages were only part of the reason they were known as the clan of "Longevity".

Danzo had also unknowingly rid Naruto of a traditional Uzumaki weakness: their temper. While it would flare from time to time within Naruto, it would not show, and that was the strongest weapon he had given Naruto. The ability to control his temper would allow him to make calm, calculated decisions while retaining the strong will of his bloodline.

Naruto was snapped from his thoughts as he listened to Danzos next words.

"Take off your mask Maelstrom. You will now be referred to by your given name, Naruto Uzumaki."

This…was unexpected and confused Naruto greatly. He knew Danzo would not ask an agent of 'Root' to reveal themselves unless it was for good reason. Though he was baffled, he did not hesitate to follow through. He understood where he stands, and he has known this fact since he could understand words. He was nothing more than an instrument to be used for Konoha's protection. His life was meaningless unless it was for what Danzo deemed was "the greater good."

Naruto proceeded to obey Danzo's words and unveiled his face. It was a charming, youthful face, one that would be sure to be the cause of many heartbreaks in the future and make certain a certain green beast chant "YOUTH!". There were no blemishes or marks worthy of mention. All that existed were his deep blue eyes and the smooth, tanned skin that fit his current age.

Danzo focused his eyes onto Naruto's and stated with an imposing voice, "You have a new mission, and a prolonged one child. Since the Kyuubi attack, the village has been restless and are in need of a scapegoat. You are to act as the Jinchuriki of the Kyuubi and become this village's deterrence towards the unease and panic and felt. You will not cause them harm under any circumstances. This is a necessary step toward our ambition for Konoha to reach new heights."

As Danzo continued to speak, Naruto spent his focus in controlling his anger. His fury grew with each word that was spoken, and as much as he wanted to unleash them, he couldn't. He wasn't qualified, nor capable of doing so. He was powerless here. Yes, he was strong for his age, but he was nowhere near strong enough to escape the clutches of Jounin level ninja, especially when Danzo was easily capable of being a Kage level ninja. He simply wouldn't survive, so all he could do was take in his words, and begrudgingly accept whatever mission was planned for him.

Through his speech, Danzo hadn't noticed any change in Naruto's demeanor, which showed how successful his training methods were. If Minato truly thought he would change his ways, he was truly blind in judgement of character. Danzo Continued, "However, we must make it believable that you are the host of the Kyuubi. It is a simple method and one that is easily capable of swaying the fragile hearts of the citizens." Danzo looked to the left and right within the shadows and said, "Fu, Torune."

With their names called, they revealed themselves to be the newest orphans Danzo had acquired during the Kyuubi tragedy. They were two of many he had received, which truly made Danzo content, knowing he would have a larger force of 'Root' operatives soon. He even saw the tragedy as a blessing in disguise.

So these are the new blood? They seem to be not much younger than myself, thought Naruto as he examined the entrance of the two new agents. A Yamanaka and…an Aburame clan member? How did he get his hands on them?

The Yamanaka clan were a well knit group and liked to keep their abilities to themselves, since abilities having to do with the mind were rare and incredibly dangerous when seeking intel. It was a very sought out skill in interrogation, and for that reason, had been kept locked in secrecy even now.

The Aburame were a bit closed off due to their abilities with insects. Though they were an honored clan, they were also a bit of an outcast since not many can accept the presence of insects without being disturbed to some extent. Hence why they secluded themselves to an extent, associating with others only when necessary.

It really made one think how he was capable of doing so without being caught in the act.

The Yamanaka was a small, young boy with orange hair tied back into a ponytail, which was traditional Yamanaka fashion. His eyes were yellow and sharp, which gave you the feel that he was a hawk hunting his prey. The Aburame standing next to him wore goggles to shield his eyes like most of his clan, with dark black hair spilling over them slightly. They both wore the usual outfit ANBU operatives were required to wear, along with a tanto sword on their back.

They Proceeded to walk towards Naruto, unsheathing their swords. Naruto did nothing but stay in position. He did not believe that Danzo would kill him after assigning him a mission that was so 'important' to the development of Konoha, which meant the blades served another purpose. Though, it was a bit ominous how they seemed to be dripping some sort of acidic solution.

The two orphans proceeded to slash across Naruto's face six times in total. Naruto felt a burning sensation across his cheeks, but paid it no mind. He had endured much worse than these small scratches.

Once Fu and Torune completed their task, they sheathed their weapons and returned back to the shadows. As they disappeared into the darkness, Danzo spoke once again, "The marks that have been left on your face resemble that of whiskers on a fox. This will be the symbol that marks you as the bearer of the Kyuubi. They can not be healed due to a special composition that is capable of scarring the skin of even the toughest of Uzumaki. With this all said, you will live in an apartment on the other side of the village and proceed to have a 'normal' life."

Danzo proceeded to turn around, and as he prepared to shunshin away from his position, he looked back to Naruto and left him with only a few words, "You are dismissed."

With those words, everyone aside from Naruto himself had disappeared, leaving him to his thoughts. His teeth gnashed slightly and his fists clenched, but quickly disappeared as soon as it came. He was already aware of his worth, but now he wasn't even a soldier. He was meant to be a punching bag for the distressed populace of Konoha…and for what? To ease their minds and aching hearts? He was aware of the hardships Jinchuriki go through, and even if he wasn't a true one, he was still going to be the acting Jinchuriki, which may as well be the same.

Naruto slowly rose from his position and shunshined away, preparing himself for the onslaught of rage he was sure to receive from the village, for no reason other than being a convenient source of blame.

-Flashback End-

Naruto frowned slightly at the memory, but it was worthless to think about such things now.

His eyes narrowed as he stuck out his tongue, which revealed the seal mark all 'Root' operatives were required to bear so information could not be spread. The seal showed five bars across the tongue with two being broken at the bottom. He had tried studying the seal in order to find a way to break it, but he was honestly lacking in the sealing arts. His ancestors would truly be ashamed.

This was not due to lack of study on his part though, it was due to the lack of materials in the sealing arts within Konoha. The majority of the sealing arts were within Uzushiogakure, and any sealing arts within Konoha were being protected by their respective clans.

The Hiraishin was protected by the fourth Hokage, the caged bird seal was protected by the Hyuuga, Jiraiya was always out of Konoha due to…studying various subjects of the opposite sex, presumably to have a more accurate understanding of human anatomy, as well as building a tolerance to seductive techniques…yeah…he was sure that was the reason. Danzo himself would never reveal the truths of his seal, since that was his primary defense for secrecy. In other words, he was stumped in how to proceed.

Funnily enough, he was able to understand the seal, but he didn't know the right methods for disarming it without causing irreparable damage. He had always found it strange how he just seemed to 'know' how a seal would work. It seemed to be a trait of the Uzumaki, but he never understood how that was so. Of course, this was limited to simpler seals, but after being in contact with his current seal, he was capable of deciphering it quite a bit.

He was able to understand that each bar represented the five senses a human possesses. Sight, hearing, touch, taste, and smell. The two broken bars at the bottom symbolized the senses that have been forbidden, though it seems the seal isn't perfect.

He could see that the original design was meant to silence an individual permanently, as well as completely eliminate any sense of pain an operative may feel. It was also meant to kill the 'Root' member should they try to fight against the seal. This would create the 'perfect' soldier, who was incapable of passing along any information and breaking their will through torture and interrogation. However, it seems Danzo isn't as skilled in the art of sealing as the Uzumaki. The structure was much too simple, so he was only capable of limiting what an operative was capable of speaking about with the only repercussions being paralysis rather than death, and could only numb the pain a 'Root' member feels slightly rather than completely.

Though, Naruto figured the seal marker couldn't become too complex due to the limited size of a tongue. Anything more complex would require a larger 'canvas', so to speak. The area of a tongue did not allow for complexity, but did allow secrecy, so he figured that was the tradeoff in its application.

But despite his knowledge of the seal, he simply couldn't figure out how to disarm it. Creating seals were one thing, but deconstructing required precision, knowledge, and experience. All of which he did not have due to the limited resources in Konoha.

Shaking his head of his thoughts, Naruto lifted his battered body and proceeded to enter the broken gate into Uzushiogakure. Perhaps, he can find his answers somewhere in there?

A/N: As you can see, I am just creating the setting of the story. There was a lot of detail in here which may need to be understood for any future sealing theories I bring up. Now that you had a read-through, I want to explain what I'm trying to do with this story.

I always saw the seals could have been a much bigger part of the Naruto story, and as you can see so far, I am trying to create my own theories and explanations of how seals work. That is what is going to be the main part of Naruto's strength. While seals may seem boring, I feel like you can be a lot more in depth with seals in comparison to jutsu. You can imagine things more and be more creative.

I know some of it was a bit of an info dump, but again, I am just trying to set the pace for hte rest of the story. I'm up for good criticism, since this is actually my first work being released. Yes, I am indeed what you would call a "Noob" and "Amateur".

Do I suck? Probably. If that is the case, let me know along with a reason. I'm trying to improve myself, and that can only be done with constructive criticism and the truth.

I hope you enjoyed it so far, if not...then sorry? I'll do better. Shia Labeouf is counting on me. In his wise words he has spoken, "Just, DO IT!"

That will be all from me.

~Stay Cool, but don't Freeze