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Senju Naruto, Prologue

"Tsunade-hime! What brings you here?" The newly appointed Hokage says, greeting his predecessor's student. Beside him on a bar stool, is the Toad Sage slumped over snoring. The Hokage was very cautious, making sure his flame-trimmed coat did not touch the Toad Sage's slobbery puddle.

"Shouldn't I be asking you that question?" She quipped, while taking a seat unsteadily on the other side of the unconscious Sannin. "After all, this town is almost two days away from Konoha? And you are the Hokage"

"You're right.." Minato scratched the back of his head out of embarrassment, "I should probably get back now, the baby is due tonight. I would hate to leave ero-sennin though.."

"Such a fitting name," Tsunade laughed, "I will take care of him. Say hello to your wife for me, I would hate for anything to go wrong with the operation and you not be there"

"Ah thank you, I will see you soon." Minato nodded and disappeared

Today was an exciting day for the newly appointed Hokage. It was the day he was expecting his newborn Son. Many were scared that during childbirth Kushina's seal would come loose, and the Kyuubi would wreak havoc on the village. So, as a precaution Kushina was escorted to a remote location, a little distance away from the village.

"Just in time, Minato," Biawoko Sarutobi said with a sweet smile, "Kushina is going into Labor now, I was just going to send for you."

Once the baby was out, Minato erupted in cheers and shouted. "May I hold him!"

"Settle down." Biwako said, shooting Minato with a cold look. "Kushina you can get some rest now, I am going to give the baby a nice bath."

"Ero-sennin and Tsunade-him sends their regrets that they couldn't be here," Minato explained, "Naruto is a very beautiful boy, you did a great job Kushina"

Kushina smiled. "I am so tired but I just have this horrible haunting feeling"

Just as Kushina finished her sentence, Dekai said there was an unknown person approaching the entrance. Minato was confused, "How could an unauthorized person get past the ANBU?"

Just then Biawo and her midwives fell to the floor unconscious. Naruto was in the hands of a masked man, with a Kunai on his neck. "Yondaime-sama, step away from the Jinchuriki"

"Cmon.. calm down, let go of the baby." Minato said slowly backing away from Kushina. He signaled Dekai to back away from Kushina aswell.

Suddenly the man dropped the baby on the bed, and grabbed Kushina. He teleported away with the now weak Kunoichi, "Dekai! Inform your father of the death of your mother, then if you want you may join me in battle against this man."

Minato took up his son before teleporting to his safehouse. He began to prepare for battle, he knew that if the Kyuubi was released there would be an extremely horrible consequence for Konoha, "You'll be safe here my son."

^With Kushina^

"Why is this happening to me.." Kushina thought to herself. This wasn't the first battle she has ever been in, but this one felt different. Like it was the end for her, this man's killing intent is extremely high. "What do you want with me?"

The man chuckled, "It is nothing personal, I just want the Kyuubi inside of you"

He performed some kind of Jutsu which caused a black ink looking substance to leak from Kushina's Seal. She felt Kyuubi getting ripped out of body and Chakra stream, she screamed in agony as the pain continued. Despite being weak due her pregnancy she tried with all her might to keep the Kyuubi within her.

The seal was almost broken, and the man just teleported her to the outskirts of the village. She knew once it was released, he was going to use the tailed beast to destroy her village. "Minato.. Hurry"

Poof! A cloud of smoke appeared as if the Tailed Beast had just been summoned. People from inside the village could see the large tailed beast, with his red sharingan filled eyes. Alarms were immediately sounded, an attack on the village was imminent.

Minato was too late. The Nine Tailed Fox was rampaging throughout the village, but he was just in time to use his Hiraishin seal to seal away the Biju Bomb which was close to destroying the Hokage Monument. He teleported to the front lines, he witnessed the many casualties the Kyuubi was causing and felt guilty.

"I am here to help," the Former Hokage said, "Finally I won't feel old!"

The young blonde chuckled. "It is time."

"Kuchiyose no Jutsu! (Summoning Jutsu)"

A large toad appeared in a puff of smoke. "Gamabunta.. Help the Sandaime push the Nine tails back!"

Gamapunta, the Chief of the Toad of Mount Myoboku, was summoned. "Hey there Minato! Why are- WHAT THE HELL who let that fox out!"

Minato chuckled. The masked man suddenly appeared at a distance for them, "Nobody is getting past me."

"Sandaime-sama, go forward." Minato said, creating hand seals for a big fire ball release.

"Minato Senju, Konoha's yellow flash." the Masked man chuckled. "You won't be able to suppress the Kyuubi, the Hidden Leaf will be no more!"

Hiruzen and Gamabunta were doing their best to hold back the Kyuubi. "Anbu! Summon the Sealing Corps!"

"Hai!"

The masked man wasted no further time. "Doton: Dosekiryū (Earth Style: Mudslide Jutsu)" he punched the ground causing a large mud slide to appear streaming towards Minato. Which was quickly countered by Kakashi's Technique, "Raiden! (Lightning Transformation)" Kakashi slammed the technique into the floor effectively canceling out the Mudslide.

"Kakashi of the Sharingan.." the Masked man says impressed.

The Masked Man did the hand seals for the Fireball Jutsu but little did Minato know he was using the Jutsu as a distraction to officially kill Kushina. Minato's face was filled with fury, he summoned his multiple Kunai and threw them at the masked man.

Kakashi dashed towards the man with a Chidori activated. When the blow landed on the Masked Man, he erupted in laughter. "You fool! Don't you know a Ninja must never enter a battle without knowing what they're getting into? Now you shall pay!"

His celebration was cut short, because Kakashi's Chidori was only a distraction to throw a Flying Raijin marked Kunai. "Teleportation.. Complete"

"Rasengan!" a large sphere of Chakra was slammed right into the back of the Masked man, causing part of his mask to fall revealing a Sharingan.

"Argh!" He screamed in agony before disappearing.

"Minato-sama!" Kakashi exclaimed, "The Kyuubi no longer has a Sharingan in its eye, It seems that man was controlling it."

"Am I late to the party?" Jiraiya said with a grin.

The team launched towards the Kyuubi. Hiruzen used his staff to push the nine tails back, Gamabunta used his sword to distract him.

"Ranjishigami no Jutsu! (Wild Lion's Mane Technique)" Jiraiya's hair began to extend, attempting to wrap around the Kyuubi.

"Minato! Throw me one of your Kunai!" the Elderly man grabbed the Kunai, "Kunai Clone Technique!"

As the kunai flew towards the Kyuubi, Minato teleported himself and Dekai to the Kyuubi. Placing paper bombs, causing the Kyuubi to fall. "Now! We need to seal him!"

Minato froze. "We won't be able to hold the Kyuubi down for long without mass casualties, let me bring the Kyuubi to the grave with me."

"No Minato.. It would create an imbalance of power in the Shinobi Villages" Hiruzen replied. Each of the Shinobi villages long ago were given Tailed Beast that could be used to boost their Military prowess. Konohagakure has the strongest, and they would become a weaker nation without.

"I know what to do." Minato disappeared in a yellow flash, arriving in his bunker. "My son, I am sorry that I am going to leave you here. You'll be in safe hands for sure, I will make sure of it." He grabbed his son and teleported back to the scene, summoning an Alter and placing his son in it. He was going to use his son as the living vessel of the Nine tailed fox.

Minato exchanged looks with Kushina, both knowing what was about to happen. The moment was cut short when the Kyuubi attempted to stab Naruto using his nails, causing Kushina to get in the way. "You have already claimed so many lives, I won't let you do any more harm.. Kyuubi"

"The village needs a Hokage, and my time has already come. Let me take care of this, I know you want to use Naruto as the next vessel. So I will only give him half of the Kyuubi and take the other half to the grave with me." Hiruzen replied

As Hiruzen began the hand signs to seal the Kyuubi, he was struck with one of the nails of the nine tails. "Minato.. I won't be able to survive. You must live on! Hakke no Fūin Shiki (Eight Trigram Sealing Technique)"

The nine tails was quickly shrinked and the yang half could be seen getting sucked into the body of Naruto, which brought the elderly Hokage a smile to his face. "Where tree leaves dance... one shall find flames... the fire's shadow will illuminate the village... and once again tree leaves shall bud anew."

He fell to the floor, lifeless. A fitting end, for a fitting leader. His former students, Minato and Jiraiya gathered around his body paying their respect to their fallen teacher. "That old man really was a strong man"

"And I thought I was always the talkative one," Kushina joked in between gasps for air. "Naruto, I am sorry I gave you that damned Kyuubi. Just know I love you so much, and I am so sorry I won't be here for you. Minato, please take good care of him. And ero-sennin keep away from my son with your perverted tactics! Anyways that's all from me"

One day later, Council Chamber

Minato walked into a room filled with representatives from every clan. The Sarutobi, Senju, Uchiha, Yamanka, Namikaze, Nara, Hyuga, Aburame, and Akimichi clan. The other minor clans were also present. They were bickering amongst themself, arguing about the fact that the Kyuubi had a Sharingan in its eyes.

"Enough!" Minato shouted, getting the attention of everyone in the room. "We just lost our leader, Hiruzen Sarutobi as well as the Jinchuriki of the Nine Tails Kushina Uzumaki. The least we can do is have a meeting filled with order."

The room went silent until Shikaku Nara spoke up. "On behalf of the Nara Clan we extend our gratitude to the members of the Senju and Sarutobi Clans. Now the most pressing matter on our agenda is the Uchiha who controlled the Kyuubi.

Fugaku Uchiha, the Clan head of the Uchiha Clan, rose from his seat angered by the accusations. "The Uchiha clan had nothing to do with the attack against this village! Please do not forget we are one of the founding members of this village!"

Minato nodded his head. "Fugaku-san is right. We have no proof other than the fact that we seen a Sharingan that it was an Uchiha."

"Hokage-sama if I may?" Dekai said, getting up nervously.

"Sure, go ahead."

"I checked with our Ninja data book. There are no known rogue Uchiha Clan members, nor any known defectors of the Uchiha Clan other than Madara Uchiha who has been dead for many years." Dekai continued.

"So what!" Fugaku shot an angered look across the table. "I will not sit here and tolerate any more accusations. With that being said, I am leaving this meeting. Congratulations Minato-san on your promotion to Hokage."

The entire council watched as Fugaku got up and left. Just because he left, it did not mean discussions were over. Minato still had important decisions to make, regardless of the circumstances presented in front of him.

Danzo Shimura, one of the village council members broke the silence. "I suggest we open an investigation on the Uchiha Clan. And in the meanwhile we should have their clan relocated to the outskirts of the village."

Minato sighed. "Is that the only outcome?"

"Hokage-sama, I recommend the same thing as Danzo. This should take effect today, and the investigation can be led by Danzo. He leads the Anbu after all." Shikaku spoke. All Minato could do was nod, he was the Hokage but he also had to look out for his image as the Hokage. He knew if he objected all the other clans would agree with Danzo and Shikaku.

"Then the decision is sealed!" Shikaku exclaimed. "Let's get back to rebuilding Konoha, you are all dismissed."

Everyone rose from their seats to exit the room. Only to notice Fugaku was standing right outside the door. He later disappeared right in front of them, his angered expression on his face scared half of the council.

Same day, Nightfall, Root Hideout

A young Uchiha jounin, no older than sixteen years old. Made his way down the steps of the Root hideout, the root being the hidden part of the Anbu Black Ops. This jounin was none other than Itachi Uchiha, a strong member of the Uchiha clan.

"Itachi-kun," Danzo started, "I am glad you made it."

He knew a meeting with Danzo could only mean one thing. Death or a mission so secretive not even the Hokage could be made aware. He often didn't agree with Danzo's ideals, but he did what he could for his village. "You summoned me?"

"Yes.. yes." Danzo said, chuckling. "I was made aware about the pending Uchiha Coup. Many are speculating that they were responsible for the Kyuubi Release."

"Danzo-sama, I can assure you. No Uchiha was directly responsible for last night's attacks" Itachi replied.

"That's what Fugaku told us as well, but I am worried about the image of the Village. Say the speculations spread and any information regarding the coup spreads as well, villages would exploit our weakness."

Itachi let out a cold sigh. "And what is your plan, Danzo."

"I want you to get rid of your clan." Danzo answered. "You can keep Itachi and Sasuke alive, but the rest of the clan has got to go."

The young jounin was shocked. "And if I decline?"

Danzo chuckled. "Everyone in the Uchiha clan, including you, shall die. By someone else."

Itachi bowed his head. "I will get back to you"

He disappeared even before getting confirmation. He wanted to go see his long time friend, Shisui Uchiha.

One Hour Later, Forest of Konohagakure

It was late at night but a normal time for Itachi Uchiha to be up. He has been serving in the ANBU for the past two years, much to his friend Shisui Uchiha's objection. He knew that there was always an evil side to the ANBU, especially with Danzo Shimura leading it, and today Itachi discovered he wasn't wrong.

"What's up Itachi? It looks like there is something wrong?" Shisui was concerned for his longtime friend. He knew Itachi was a genius and that meant he was always thinking, but today he seemed out of place.

"It's nothing, just a little tired that's all." Itachi answered, trying not to draw any attention to the impossible decision he has to make.

"Understandable, anyways you were missed during the clan meeting. They are planning some kind of coup, we have to stop it."

Itachi frowned. "That's why Danzo asked me to slaughter the clan."

"What!" Shisui replied. "We need to tell Hokage-sama! The Uchiha Clan is one of the founding clans he must be out of his min-"

"He may be right though." Itachi quipped. "They are causing problems in Konoha with this stupid coup, I am going to carry the mission out."

Shisui lowered his head in shame, "You're only thirteen, how could he task you with that at this young age." He was immediately interrupted by the young Shinobi, "Shisui I have a plan you don't need to do anything!"

Shisui let out a sigh. "Well you should get some rest, Itachi I will see you tomorrow."

Itachi agreed and began to walk away. His heart filled with conviction he understood the Shinobi world fully but never understood why a trusted advisor of the village could put such a burden on him. He knew he wasn't going to sleep, he was going to seek out someone to take on this burden. He felt a heavy feeling like an emergency is occurring.

With Shisui

As he was walking home through the forest Shisui had a feeling he was being followed. He stopped and clenched his fist, determined to figure out who was following him. When a voice suddenly called out, "Uchiha Shisui… You have become a liability to this village. Surrender or be killed!"

Danzo Shimura and his trusted right hand, Yoji Aburama, emerged from the shadows. "You once threatened me, but now I have the upper hand Shisui."

Shisui smiled, "You're right, you don't need to leave Itachi Uchiha alone. He can take care of himself if I dont stop you, he most definitely will."

Yoji launched towards Shisui with a Kunai drawn. Shisui blocked it with his Katana, "You're going to have to do better than that."

"Insect swarm Jutsu!" Yoji shouted, summoning poisonous insects. As they began approaching Shisui he began to weave hand seals, "Katon: Gōkakyū no Jutsu (Great Fireball technique)"

"You fell exactly for my trap you fool! This battle didn't even last that long, I wanted to have some fun"

The Kunai Yoji used to attack Shisui was quoted with poison, he felt his body tensing. He tried to fight back as Danzo got closer, but the poison and now the insects from Yoji was causing him to be paralyzed. Danzo reached his two and plucking out Shisui's right eye, making Shisui fall to the floor.

"Amaterasu"

Black flames began to emerge Yoji Aburame. "Danzo-sama! What is happening"

Itachi Uchiha appeared beside Shisui. "I am sorry, I should've gotten here sooner"

Screams of agony could be heard coming from Yoji, he fell to the floor. Once the dark black flames fully emerged him there was not even a trace of his body. This shocked Danzo, "Itachi remember what I told you. The Uchiha Clan will be killed whether it's from you or not. If you don't do it, Sasuke won't live."

Shisui tried to speak but as the poison went through his system he found it really hard, "Itachi d..dont fall for it. You can attack him" he said in between gasp. Itachi placed his hand on his friend, motioning that it would be fine. "We will let him go for now, Shisui. Remember I have a plan"

With Danzo now gone a man came out from the woods. "I thought you were lying, Itachi-kun. Danzo Shimura really wants the Uchiha Clan gone."

"Who are you!" Shisui said barely above a whisper, squinting his eyes only being able to make out a tiger mask. With crimson red eyes beneath, "You're an Uchiha? But not of this village?"

"Hmm," the Masked man said, "You're right and wrong, I am an Uchiha and I am from this village. My name is Madara Uchiha, I was exiled when my own clan casted me out although I only wanted the best for them."

"Madara?" he chuckled, "Madara died many years ago. There is no way in hell he is alive, right Itachi?"

"You're wrong Shisui-san," he said, shaking his head. "This is Madara Uchiha. He was the one responsible for the Kyuubi attack. He is going to carry out the massacre since he already has a vendetta against the Uchiha."

This was perfect. Itachi didn't have to get his hands dirty nor feel terrible killing his clansmen, he could also make sure Sasuke is okay and join Jiraiya's spy line. He was truly an intelligent young man, he was said to have the brain capacity that exceeds that of even Hashirama Senju, the founder of one of the Great Shinobi villages.

"I seen what happened Shisui.. I believe thats your name. That man Danzo has your Sharingan in his right eye." Madara said, causing Itachi to notice the blood dripping down from his friend's face. "Damn that Danzo!"

Shisui got up and walked over to a nearby waterfall. "Itachi.. I know you were given an impossible decision to make. I lost my right Sharingan so we cannot even suppress the Uchiha Clan, I want you to take my left eye and use it to serve this village."

Itachi was confused, raising his eyebrows, "What do you mean?"

Shisui removed his left eye, "take it Itachi. Do good for yourself, Madara Uchiha.. I hope you help this young man more than I ever could." He placed the Sharingan in Itachi's hand, then jumped off into the waterfall. Itachi fell to his knees witnessing the death of his friend, "Damn that Danzo! Madara.. Kill him tomorrow."

The masked man nodded.