Chapter 1: Prologue - Night of the Massacre

DISCLAIMER: This story is not mine!! Read the original at fanfiction.net "Naruto: The Uchiha Prodigy" by Rifat

==========

Uchiha Clan Compound, Konohagakure no Sato, Hi no Kuni.

A boy, age of seven years, is running through the isolated area between the buildings. It is filled with traditional Shinto styled buildings.

The boy himself is 4'3 which is considerably tall for his age. He has jet black raven hair and azure, blue eyes just like his mother. His brothers apparently did not inherit the eye color that only he and his mother shared. He has slightly tanned skin and has a lean build for his age. Slight traces of baby fat can be found on his face as they accentuate his face pretty well. He is wearing a dark blue kimono and frantically crying because he previously heard writhing, nightmare inducing screams coming from the main side of the compound.

On the back of his kimono, is a crest. The crest is that of a fan divided in two sections. The top half is red and lower half is white.

However, now the color of his eyes have changed out of pure instinct.

Just a few days ago he had learned that his remaining living brother had gone missing and was considered dead, his eyes had evolved from the traumatic news he had heard. A small opaque black dot lies in the center of his red iris. Surrounding the dot are three tomoe, lazily spinning as if they are waiting for something to happen. This eye is a rare dojutsu and is considered one of the most rare Kekkei Genkai in the history of the shinobi world. The Sharingan.

These eyes are known only to manifest in the eyes of those who belong to the Uchiha Clan. Said boy is also an Uchiha. He had awakened his at age six and trained ever since an incident changed his life. He did however hide this fact at his brother's request. His name is Naruto Uchiha. This is his story.

Naruto Uchiha was born to the lesser branch of the Uchiha Clan but he is nonetheless an Uchiha.

Sometimes though he had been treated worse than dirt because of what his father Genjuro Uchiha did. He was considered somewhat of a 'traitor' in the eyes of his fellow clansmen.

Why you ask? Genjuro and his wife Satsuki Uchiha were once considered the greatest Uchiha to emerge from the branch side of the clan since Kagami Uchiha.

When Satsuki became pregnant with their first child, she immediately decided that she would quit the life of shinobi and raise a family. She had lost her brother in a battle that caused her to awaken the next stage of the Sharingan. The Mangekyou Sharingan. However she was wise like her husband Genjuro, who had also awakened the Mangekyou, and rarely used it fully aware of the consequence that followed from too much usage of the evolved dojutsu.

After their first son was born she was over the moon as was her husband.

Their first child was Obito Uchiha. He was a kind child who had inherited his parents' traits through and through. The main difference was that he was a slow learner when it came to being a shinobi. He would wear goggles and proclaimed that he was going to be the first Uchiha who became Hokage.

He would later go on to study under Minato Namikaze one of the most up and coming elite jounins of Konoha.

Five years after that, their second son Shisui Uchiha was born.

Even from a young age he showed signs of being a prodigy. Yet unlike the normal Uchiha who would immediately gloat about this and inflate his pride so as to it could touch the sky, Shisui was rather kind in his behavior and very humble about his skills. He especially looked up to his brother Obito, who may have been weak in the eyes of the elite but to Shisui he was what a shinobi should be.

A person who never gives up and overcomes the odds.

Eight years later. The family of four received news that make them happier than ever.

Satsuki Uchiha is pregnant. Genjuro is happy that he would become a father once more, while both his sons are ecstatic to say the least. Obito was jumping in joy that he would once again be an aniki to another little guy, while Shisui was happy at the fact that he would be an older brother. Their happiness was short lived however.

An event changes the world. The Third Great Ninja War begins. As usual, Iwagakure is the cause of this once more.

Genjuro Uchiha one of the brightest Leaf shinobi to emerge was sent to the front lines and was part of one of the most important battles during the early stages of the War. During a raid in the Land of Waves, he had seen battalions of Iwa shinobi who had taken over the place and seemed to be oppressing the people. A portion of his team that he was leading had been captured by Iwa forces. Seeing that he would have to sacrifice his team, he disregarded all the rules and kicked the mission to the curb. He save the lives of fifteen chunnin and ten gennin, he had also liberated the Land of Waves but the Iwa forces understood the strategy the Hidden Leaf had played and they changed their entire tactical plan towards the Kannabi Bridge.

In other words, Konoha had blown their chance to plan a surprise attack on Iwa because Genjuro had valued the lives of his teammates and the people of Nami no Kuni more than the mission.

He was however killed in action while saving the people. His greatest regret being that he could not see his newborn son being born into the world. He was not even given a proper burial as ROOT had decided to burn his body on spot so that no secrets could be spilled, witnesses watched this and nobody protested against the fact that he would not be buried at his village.

All the honor he got was a name on the Memorial Stone in Konohagakure no Sato.

The Uchiha were outraged at the humiliation that Genjuro had brought them and had driven the family of three, soon to be four to the edge of the Uchiha Compound. Often times the fellow clan members would berate and verbally abuse the family for bringing great dishonor to the clan.

To his family however, they understood why he did it. He valued the lives of others over himself, to them he was a hero. That was just who Genjuro Uchiha was. A selfless shinobi.

Even the general citizens of Konoha looked at them with disgust because ,to their lesser knowledge, he had cost them an important victory in the early stages of the War.

Obito had often spoken up against this but the Clan Elders paid no heed as he was from the lesser branch of the family. Obito had sworn that once he became Hokage he would make sure the Elders would apologize to him and get rid of the stupid system that divides the Clan.

Sadly for the young Uchiha he never got that wish to come true. He had sacrificed himself in the battle of the Kannabi Bridge which resulted in Konoha winning the the Third Great Ninja War. Obito Uchiha was remembered as the shinobi who stayed behind and activated the explosion seals that destroyed the bridge, the right side of his body was crushed beneath a boulder but he still pulled through with the mission after his team safely got away.

Even after that the family was looked down upon, they were known as the Uchiha Lambs. Only useful as sacrificial lambs as some of the main members of the Uchiha household had put it.

Obito's legacy however had lived on through his teammate Kakashi who had Obito's Sharingan in his left eye. It was a gift from Obito to him and his family appreciated the fact that their son and brother had a true friend, who would not waste the gift and Kakashi himself had adopted Obito's way of living as a shinobi. A girl named Rin Nohara was also his friend but had died a few months after the war.

Shisui would later go on to continue his brother's wish to protect his family and the village. He was quickly recognized as a prodigy and also awakened his Mangekyou Sharingan at the age of eight after he heard his brother had died, he had previously awakened the Sharingan at age five after nearly dying because of an attack by unknown ANBU who committed suicide before they could be interrogated.

However as the darkness came to consume the family a new light was born. Three months after the war ended. Satsuki's third child was born.

Naruto Uchiha.

When Naruto was around two months old, the Nine Tailed Fox attacked and killed a lot of people in the Village. The Fourth Hokage Minato Namikaze had sealed the beast into an unknown newborn girl. He saved the village at the cost of his own life.

The village had started to suspect the Uchiha Clan, as they knew that the Kyuubi could be controlled by the Sharingan. Some of the people even called the youngest child of Genjuro a sign of calamity as his birth had resulted in an attack two months after he was born.

Naruto Uchiha was a mix between his mother and father if his looks said anything. In terms of personality he was like both Shisui and Obito. He had Obito's somewhat goofy approach to life and was always calm like Shisui. Even the verbal beratings did not matter to Naruto Uchiha. He knew that he had his mother and brother who would always be there for him. He had also somewhat of an older brother figure in Itachi Uchiha.

Itachi was a few years younger than Shisui but was his best friend. As Naruto had once eloquently put it, Itachi was not 'one of the Uchiha who had a stick up in his ass'.

Where a child had learned a term like that was beyond everyone present during the event. This had resulted in his mother chasing him comically but he was able to avoid it every time. Normally he would run too fast or use the most powerful jutsu known to children, Puppy Eyes no Jutsu.

Naruto's personality drastically changed when his mother died from a disease when he was six. This incident resulted in him awakening his Sharingan, with two tomoe no less. Shisui decided that he would train his outoto. He secretly began training him and much to his surprise he was also a prodigy, albeit one that progressed at an abnormal rate. Naruto had rarely ever used the Sharingan and could do the traditional Uchiha fire style jutsu after one go.

Only Shisui and Itachi had known about his unnatural progress. He was even considered by both those prodigies to be someone who would give them a hard time once he grew up. He was however told to hide his skills at all times by them. He agreed with them without a second question.

He had also inherited his oldest deceased brother, Obito's dream to become Hokage. He would do it for his brother and get rid of the boundaries that separated the two Uchiha family branches.

Other than Itachi, he was close to Mikoto Uchiha. She was the wife of the clan head, Fugaku. She was a very nice and kind person. She often used to tease him about how he would grow up to be a real ladies man. This came on when he accidentally blurted that if he ever got married it would be to someone beautiful like Mikoto. Realizing what he said he had gained an embarrassing blush on his face and she would often tease him to grow up so she could marry him.

Her younger son Sasuke, who was the same age as around him, was quite weird at least in his opinion. He always looked to be getting his father's attention and constantly trying to do things Itachi had performed at his age. He would also ignore Naruto for some reason.

Naruto however in general was happy despite all the shit the universe decided to throw at him. His Sharingan training went well and he had successfully mastered his two tomoe, but only Shisui knew about that part.

A few days ago he received news that Shisui disappeared and was presumed dead. His eyes changed into the three tomoe Sharingan. His entire world had been broken apart. His only family was dead. Not even Itachi was around after that.

Now, in the Uchiha Clan Compound

'Where is everyone?!' Unfortunately for the boy his questions are answered just not the way he wants.

The sight before him is what shocked him to his core. Several dead bodies. Everywhere. All the people in the Uchiha Compound were lying in pieces, or stabbed horribly as blood gushed out every now and then. He was shaking visibly and scared. He went near the body of a random person and was shaking it.

"Hey! Please wake up!'' He started crying. "What happened? Who did this?!" Naruto was wailing now. Such a gruesome sight was never meant for young ones like him.

"I did it."

A single cold voice cut through the air in the middle of the night. Naruto knew that voice all to well.

There standing in front of him with his Sharingan spinning wildly before taking on the shape of a fuma shuriken, stood Itachi Uchiha in an ANBU Uniform. His body was covered with blood that was dripping from his body. His eyes looked like they were aiming to kill him.

"Hello Naruto" Itachi said and let out a massive killing intent which resulted in Naruto's Sharingan deactivating. Naruto was shaking with fear as he fell on to his knees. His mind only raced to one conclusion. Did Itachi-nii do all this?

"I-I-Ita-achi-nn-ii... Did you do all this?" Naruto asked while whimpering.

"Yes. You've gotten a lot smarter than before haven't you Naruto?" Itachi then looked at him more carefully. "Perhaps I should kill you next considering how you're progressing."

Then Naruto's world turned black, red and white.

The Tsukyomi World

"Welcome to my world Naruto." Itachi spoke with a soft threatening voice.

Naruto saw that he was hung upside down on a cross and he saw the scene around him.

Itachi was killing the entire clan as blood spilled everywhere. It was too much for Naruto.

He then saw Itachi kill Fugaku.

But what really tore his heart apart was when he drove his tanto through Mikoto's chest. She was his guardian after his mother died and seeing that was his breaking point.

"Please stop it Itachi-nii!... Nii san.. Please help me!" Naruto cried out for his brother Shisui.

"I'm afraid Shisui can't help you Naruto." Itachi paused as the scene changed to a waterfall.

Naruto saw Itachi and Shisui standing there. Shisui's back was turned to Itachi, when Itachi stabbed him with a tanto and ripped out his both of his eyes. Shisui's body was falling into the large chasm where the waterfall was from the injuries he suffered.

As Shisui fell he looked towards Naruto and spoke.

"Why didn't you help me outoto?"

Naruto let out a scream hearing this from his only brother

Then something strange happened. The red sky of the Tsukuyomi world was starting to shatter. Itachi saw the reason as his genjutsu broke.

Uchiha Clan Compound

"Mangekyou Sharingan" Itachi muttered as Naruto's eyes changed to the shape of a four bladed scythe joined in a circle (Imagine Obito's Mangekyou with four blades instead of three) as his eyes began to slightly bleed from the usage.

"It seems that you have the same eyes as me Naruto. Yet you cannot use it yet properly." Itachi then turned around to leave. "When you are strong come find me. Then we shall see who is the strongest of the Uchiha Clan. These weak, pathetic clan members did not prove to be the challenge. Embrace your hatred only then you will be able to defeat me and avenge Shisui."

"There is no way you could kill nii-san, Itachi-nii" Naruto said in a soft voice as the bleeding had stopped and his Sharingan had deactivated altogether.

"You're too kind to do this Itachi-nii. One day you will answer everything to me. I know it." Naruto said with a sad smile and grew even more sad when Itachi turned towards Naruto. Itachi was shedding silent tears of sadness and said a few words before leaving.

"..."

"Goodbye Outoto."

Itachi disappeared into a flock of crows.

The darkness began to take Naruto. But then something else happened. He could feel the presence of something nearby. It felt all to familiar, yet unknown at the same time. He then heard a swirling noise before he fell unconscious.

The next day the Village Hidden in the Leaves heard the tragic news. The Uchiha Clan, one of the founding clans of Konoha, had been wiped out by Itachi Uchiha, who wanted to prove his strength and presumably had cracked under the pressure of being an ANBU Captain at such a young age. He left behind two survivors.

His own younger brother Sasuke was now Clan Head and another member from the branch clan, whom everyone recognized as the son of Genjuro who had shamed both the clan and the village.

From then on the age at which the students would enter the Academy had changed. Now they would be admitted nine and would graduate at fourteen. The Academy standard had also considerably dropped to a more basic level to the point where even civilians could become genins without any problems. A foolish part on the Council's part, however the standards for the shinobi exam had been dropping for some time now. And not just in Konoha but the other major shinobi villages as well.

Peace was deteriorating the overall skill shinobi had.

Konoha Hospital

Naruto had woken up and was interrogated heavily by the shinobi as to what happened. He explained briefly that he had entered the compound after having ramen for the first time at Ichiraku's. He went inside his home and heard screaming coming from the main compound. He went in to find the dead bodies and Itachi had put him under a genjutsu.

When asked about the blood they found on his face, Naruto put on his best poker face that Shisui and Itachi had taught him and explained that he had accidentally stumbled onto a dead body without looking properly and fell face first onto the body.

They believed that the seven year old was not lying about such a traumatic event and left him to recover.

Sasuke on the other hand had gone on to bubbling out everything that had happened. He was later treated like a prince. 'The Last Uchiha' of noble birth. How the village would treat him like a glass doll if the Civilian Council had anything to do with it.

Naruto was a stain on the existence of the Uchiha. A branch member but now one of the last two loyal Uchiha left. Now they treated him a bit nicer as he had gone through a significant trauma.

Naruto still did not want to get out of the hospital. He wanted to fake his injuries to remove some suspicion from him. He needed to pretend he was a weakling. Shisui had drilled this into him a long time ago.

"A true shinobi always hides his true skills and his greatest weapon is deception" The wisest words Tobirama Senju, the Second Hokage ever spoke.

He went to the bathroom and channeled chakra to his eyes as they changed into the Sharingan.

He channeled even more and they changed shape as it took the form of a four bladed pinwheel. It was mesmerizing to Naruto but he felt significantly tired and his eyes hurt just a little bit at a time.

He came out of the bathroom and lied down on the bed. He looked up at the white ceiling.

"Itachi-nii... I will find out why you did this." Naruto said, not knowing how his life had been set on a course from last night.