Hello! The beginning of the story can remind you all of another story "Naruto: The Uchiha Prodigy" made by Rifat, but there are only a few things that will be similar.

Disclaimer: I don't own Naruto

Chapter 1

A seven years old boy was running through the almost empty streets of Konoha. The boy himself was 4'1(1.25m). He has long, black, spiky hair. His eyes are onyx black, exactly the same as his brother's, mothers and fathers. He has slightly tanned skin and a lean build for a kid his of his age, thanks to his training with his older brother Uchiha Shisui. However, his trademark characteristics are the three whiskers on each of his cheeks, which shows that he is a Jinchuriki of Kyuubi no Yoko. The boy was wearing a dark blue, high-collared, long-sleeved shirt, with an Uchiha Clan's crest on the back, black shorts, which went down to his knees. He also wears blue shinobi sandals with an opening for toes.

Uchiha Naruto was born in the main branch of the Uchiha Clan. His mother, Uchiha Yumi, was sister to Uchiha Fugaku, the current head of Uchiha Clan, thus making him a possible Clan head, if Fugaku's son, Uchiha Itachi, didn't want or could not be the next Clan Head. Naruto's father, Uchiha Sasuke, was the son of Uchiha Kagami, Sandaime's best friend. When Sasuke was born, Kagami decided to name him after Hiruzen's father. Fugaku also wanted to name his second child Sasuke, but he and his wife, Uchiha Mikoto, decided not to have a second son. Naruto also had a brother, Uchiha Shisui, who was eight years older than Naruto.

The young Naruto also found a brother figure in Itachi, who was a few years younger then Shisui. The three of them would often train together, even though Naruto was much younger than the two, he always went with them to train.

Uchiha Naruto was two weeks old during the Kyuubi's attack on the Village Hidden in the Leafs. During the attack, Uchiha Sasuke died as he was one of the Shinobi's who was on the battlefield and tried to stop the Tailed beast. Unfortunately for Naruto, he was the only newborn at this time and Yondaime Hokage, Namikaze Minato, had to seal the beast inside of the Uchiha to save the Village. Good thing was that no one besides the current Hokage, Sarutobi Hiruzen, his two advisors, Naruto himself and each current Clan Head. And to this, Sandaime made a law that nobody is to talk about this, otherwise, they will be killed.

Naruto was a mix between his mother and father. He was very goofy and there was nothing that could change his good mood, exactly like his mother, but he was also smart and was able to keep his emotions in check if he needed to.

Sadly, Naruto's personality has changed drastically when his mother died from a disease when he was five. That was also the day when he awakened his Sharingan, with two tomoe in each eye., since then, both Itachi and Shisui took Naruto's training seriously and had pushed him to his limits. When Shisui's younger brother had learned that his mother died, he became pretty much like Itachi. Calm, serious, never showing his emotions to anyone. At least that what everyone who saw him thought. Naruto didn't become cold, he was still the same goofy kid, but he simply didn't show it to anyone he didn't know.

At age of six, a few weeks before he became seven, Naruto was able to master his Sharingan under the guidance of his two older brothers. Both of the teenage Uchiha's were proud of their younger brother because he was the youngest Uchiha in the history to ever master the Sharingan. When Fugaku heard about this from his son, he said that Naruto a Genius, even for the Uchiha standards, exactly like Shisui and Itachi, of course, this news spread very fast and soon almost everyone in the Village knew about the new upcoming Genius of the Uchiha Clan.

A few minutes ago, the Sandaime had requested Naruto in his office, he said that he had some news for the young Uchiha. When Naruto arrived, the third Hokage told Naruto that his older brother Shisui was on a mission, but the mission went bad and Shisui sacrificed himself to save his teammates. After hearing this, Naruto's world had been broken apart. His only family died and for two months even Itachi wasn't too much around since he had many ANBU matters.

Now, Naruto was running through the almost empty streets of Konoha, since it was already late and everybody was either home or at some bar, drinking with friends. The boy was hurrying to the Uchiha compound since he wanted nothing more to close himself in his room and cry his heart out, even though he promised himself that he wouldn't cry anymore.

As he arrived at the gates of the compound he didn't see any guards. This wasn't unusual, but it happened very rarely. As he walked through the streets, he noticed that it was very quiet. As he walked for another few meters, he saw someone laying on the ground. When Naruto ran to him, he could see that the person was lying in his own blood.

'Who could have done this?' Naruto asked himself as he runs towards his home. On the way there he could see more and more bodies, everyone around him was dead. As he neared his house, which was next to the Clan's head's, he could hear something splashing on the ground from Itachi's house. Without any second thought, he rushed towards the place where he heard the noises with his Sharingan active and a Kunai, which he picked from the ground, in his hand. As he was about to enter the garden of the house, he heard the door open. The next thing he saw made him freeze.

In front of him was Uchiha Itachi, his older brother figure, with a Tanto on which was blood. He also was wearing his ANBU clothes, which were also in blood. Itachi looked at the stunned form of Naruto and smirked inwardly.

'Everything according to plan, Shisui' Itachi released a massive amount of killing intent, which resulted in Naruto's Sharingan deactivating.

"I-Itachi-Nii, w-why?!" Naruto shouted in anger, fear, and confusion. Itachi raised his eyebrow at the question, still releasing the KI.

"To measure my power, Naruto-kun. Here, let me show you," he said in a calm, yet cold tone. Suddenly, Itachi's Sharingan morphed into a three-bladed Shuriken and he looked into Naruto's eyes

"Tsukuyomi!"

Tsukuyomi world

Naruto suddenly found himself in another world, where the moon and sky were red, but the ground was black. While Naruto was looking around, cross materialized behind him and he was chained on the cross. Not a moment later, Itachi appeared in front of him with an impassive look.

"Welcome to my world, Naruto-kun. Here I control everything, even time. 72 hours here are merely 5 seconds in the outside world. I will show you now what happened tonight," The older Uchiha said and the world changed into the Uchiha compound. A moment later, no matter where Naruto would look, he would see Itachi killing everyone, blood spilling on the ground and buildings. Even when Naruto tried to close his eyes, they would open themselves. The young boy couldn't bear it anymore and he started to shout.

"Itachi-Nii stop this! I beg you... please stop it! Nii-san help!" Naruto shouted as tears flooded from his eyes.

"I don't think that Shisui will be able to help you. He is dead, do you remember or should I remind it?" Itachi asked and the scenery changed into a forest where a group of five was followed by at least twenty other persons. Suddenly one of the five stopped and took out a Kunai. The single person tried to fight, but he was overwhelmed, but instead killing him, the twenty took him and started torturing him.

"NII-SAN!" Naruto shouted and the sky started to break and then it shattered into pieces.

"Mangekyou Sharingan," Itachi said with a small smirk on his face as he looked into Naruto's new eyes. A red six-pointed star on a black background with a single black circle in the middle. (AN: Like Sasuke's in canon). Naruto looked at Itachi with his new eyes which started to slightly bleed from the overuse. 'Everything worked out. Now it is up to you, Shisui' Itacho thought as he took out a scroll and tossed it in front of Naruto, who was slipping into unconsciousness.

"I-Itachi-Nii... why?" Naruto asked, fatigue clear in his voice. Itachi chooses to ignore the question as he slowly started to walk away. A moment before he had to leave, he turned around, making Naruto see as a single tear of sadness fell from his eye.

"Goodbye... Otouto," He said and dissolved into a murder of crows, which flew away, leaving Naruto alone. The black-haired boy could hear steps, but he had no energy left and passed out.

On the next day, the Village hidden in the Leaves heard the tragedic news about one of the strongest, if not the strongest Clan in Konoha. Uchiha Clan has been murdered by Uchiha Itachi who, by the assumptions of the Villagers, had cracked under the pressure of being ANBU. There was only one survivor, Uchiha Naruto, son of Uchiha Yumi and Uchiha Sasuke, brother of Uchiha Shisui.

Two days later, Konoha hospital

Naruto opened his eyes just to close them as a lamp was being above his eyes. He let his eyes accustom to the new light and started to slowly open them again. When his eyes were open he slowly sat up and looked around to see that he was in a hospital room. Naruto turned to the door, which he heard that was opened by someone. When the door was open, it revelated Sarutobi Hiruzen.

"Hello, Naruto-kun. How are you feeling?" Sarutobi asked as he sat on a chair next to the black-haired boy's bed.

"Good morning, Hokage-sama. I feel good," Naruto said with a sad smile. Hiruzen smiled seeing that the boy won't become some emo, revenge wanting, brooding brat.

"Naruto-kun, I have a few questions for you," Sandaime said. Naruto nodded and Sarutobi asked his first question. "Naruto-kun, what happened?" He asked.

"After leaving from your office, I went home and there was very quiet in the compound. When I was about to enter my house, I hear something happening in Mikoto-Oba-chan's house so I went to see what was happening. When I got close Itachi-N... Itachi came out and put me under some Genjutsu in which he showed me how he killed the Clan and then how someone was torturing Nii-san and then I was lying on the ground and passed out," Naruto asked truthfully. Sandaime nodded his head.

"And what can you tell me about the blood that we found on your face?" The aged Kage asked. Naruto thought about that for a moment before his eyes widened.

"I can tell, but if you promise to keep it a secret," Naruto said and Hiruzen nodded with a slight smile. After seeing that Sandaime agreed, Naruto closed his eyes and activated his Sharingan and showed it to the third Hokage. A moment later, the Sharingan morphed into its next form.

"M-Mangekyou Sharingan!" Hiruzen exclaimed, with shock written all over his face. Naruto nodded and deactivated his Sharingan. After clearing his throat, Sandaime took out a scroll from his sleeve. Naruto eyed the scroll curiously.

"What is this scroll, Hokage-sama?" The young boy asked and the old man nodded.

"We found you lying unconscious in front of the scroll. We opened it, but for us the scroll is blank. It looks like only a person with a Sharingan will be able to read the content of this scroll," Hiruzen said as he placed the scroll next to Naruto. "Well, Naruto-kun. I will be going now. Remember, if you will need something, just come to my office," Hiruzen said and left the room. Naruto opened the scroll and activated his Sharingan once more and now he could easily read what was inside.

'Dear Naruto-chan.
If you are reading this, that means I am dead and Itachi probably gave it to you. First, you must know that what Itachi did was not what it looked like. In reality, the Uchiha Clan wanted to do a coup d'etat. Hokage-sama tried to negotiate, but the elders of our Clan thought that they would be able to defeat the entire Village. After the negotiations went bad, I and Itachi took a mission, to eliminate the Uchiha Clan and leave the Village as rogue Ninja's. Unfortunately, I didn't make it, so it all fell on Itachi, who I gave a mission to awaken your Mangekyou before he leaves. Now you are probably mad at me for doing this, but you must understand that you will need the power in the near future. When you awake your Mangekyou, go to the Hokage and tell him that you want an eye transplant. I left eyes of our mother in our secret seal at our home. They will be safe there. I know, I know, you don't understand a thing from what I wrote here, just go to the Naka Shrine, everything will be answered about the eyes there. Now, I also left a few more scrolls for you at the seal. Alright, coming to the more important things. There is a person in the Village that you should never trust. Shimura Danzo. No matter what he would want with you never listen to him, the best avoid him with everything you can. Also watch out for him ANBU, also known as ROOT. they look the same as normal ANBU but on their masks is always Kanji for 'Ne'. Their reason why I and Itachi took the mission is that the Uchiha Clan thought that they were a god amongst mortals. This stupid belief made them arrogant and they tried to revolt. We were allowed to let live those, who we believe can gain the pride of the Clan back and will not believe in their power. or at least something like that, Itachi told me to write it. Well, don't hate the Village, they did it to save countless lives and prevent a civil war. I guess that is all I want to tell you. I am sorry that you will have to live alone, but I believe in you! You are strong Naruto and me, mother and father will be watching over you the whole time!

The best brother in the whole world. The biggest legend in the elemental nations. The best Shunshin user on the continent. Brother of the next Shinobi Legend.
Uchiha Shisui'

Naruto watched as a single tear fell on the scroll, before closing it and putting it on a small table, which is next to his bed. Naruto laid himself on the bed and started to order everything that happened in the last 24 hours in his head.

'And to think that the academy starts in two weeks. Two free weeks for training to bring back the pride of the Uchiha Clan' He thought and slowly went back to sleep.

And cut! So how does you guys like it? If you have any ideas for pairing write them in review's and I will choose them until the third chapter.

Yo!