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Konoha Reborn

Summary:

What would have happened if the night Itachi Uchiha was assigned to slaughter his family, a mysterious stranger arrived at Konoha to change the fate of the village and the Uchiha clan?

Notes:

(See the end of the work for notes.)

Chapter 1: Changing a Fate

Chapter Text

“Itachi, you know what must be done in order to keep Konoha safe,” said Danzo matter-of-factly, “the Uchiha clan must either bring a halt to their plans for a coup or they must be eliminated.”
The Hokage, Hiruzen Sarutobi, spoke up then, “Danzo! You should not speak of such things in front of Itachi!”
“Hiruzen!” shouted Danzo, “Itachi is a member of ANBU; he knew the conditions of becoming a member of Konoha’s black operations division. He will…”
At that moment the door to the council room burst open and a tall man with long, dark brown hair and a handsome face strode into the council room, his eyes closed as if he were enjoying some particularly good music. Danzo, Hiruzen and Itachi were quick to respond and were standing in a line in front of the village elders, kunai at the ready.
The tall stranger snickered then and opened his eyes revealing something that made everyone, including the young Itachi, gasp in shock. The man in the doorway possessed something that not even Itachi had, the Eternal Mangekyou Sharingan.

Itachi was especially shocked, he had not realised that his clan had members that were unknown to him. On top of that he did not know of any members that had the Eternal Mangekyou Sharingan other than his best friend, Shisui Uchiha.
“Itachi! Have you betrayed us?!” accused Danzo, “Is your clan making its move now?”
“Danzo-sama…” but before Itachi could finish what he was saying, the man at the door laughed again, this time as if he found Danzo’s words to be particularly amusing, as if he were a child trying to explain away some sort of mischief.
“No, Danzo Shimura,” said the man at the door, “I am not a member of the Uchiha clan.”
Itachi paled, anger rising in his gut, “Then why do you have the Mangekyou Sharingan?!”

 

The man smiled again, “My grandmother was a member of an exiled branch of the Uchiha, my father was a member of a clan that Hiruzen-sama should be very familiar with. A clan that sent its last daughter to be fostered here and to become the new Kyuubi Jinchuriki many years ago, or don’t you remember my face Hiruzen-sama?”
Realisation dawned on Hiruzen’s face, “So you were that little boy that came with Kushina and her parents to leave their daughter here all those years ago.”
“Not quite Hiruzen-sama,” said the man, “I was, and still am, Kushina Uzumaki’s elder brother, Nagato Uzumaki and I have come here tonight to stop the extinction of a clan that I share blood with as well as to return to Konoha and reclaim my nephew from the darkness and sorrow that you have left him in.”
Hiruzen was the first to lower his weapons, Itachi doing so next and Danzo grudgingly followed suit. After they had lowered their weapons Nagato closed his eyes and deactivated his Sharingan and they became a pleasing merlot red colour.

 

“What do you propose?” asked Hiruzen, his desire to preserve an old and powerful clan, loyal to Konoha urging him on.
“Let us sit down and discuss this then,” suggested Nagato. Hiruzen motioned for one of the servants in the room to bring a seat, when the chair was brought Nagato looked at Hiruzen with irritation, “May I ask why Itachi has no seat?”
Hiruzen was taken aback by this question, but gestured for another chair to be brought. Once they were all seated at the table the elders were seated at, Nagato finally spoke,
“My mother and father kept a close eye on Konoha after they left my sister here. They had eyes and ears in nearly every clan, including the Sarutobi, Senju, Shimura and Uchiha clans. They kept us informed of the goings on in Konoha and of my sister’s progress. After my parents died in a surprise attack by shinobi of Kirikagure, I was left to oversee my clan’s shrinking powerbase and its scattered family members. I took to the task and turned my clan around. We have grown since then and have thrived. However, just before my nephew was born, my spies in the Shimura and Sarutobi clans became silent. Then one after another, all my spies in Konoha either clammed up or disappeared, except for the one in the Uchiha clan. My spy has kept me abreast of what the Uchiha have been planning and what has happened to my nephew since his parents’ deaths.”
Nagato looked Hiruzen dead in the eyes and said with barely disguised anger in his voice, “I am not pleased at all, Hiruzen, not pleased at all.”

 

Hiruzen averted his eyes, shame grasping him from deep in his gut. He had not given Naruto the kind of care that he truly deserved and had been content to keep his true heritage a secret, simply because it was more convenient to allow the boy to live in ignorance of his family and true power.
Hiruzen swallowed, holding back tears of shame and regret and asked Nagato, “What would you have me do to end this threat to the village?”
Anger still prickling in his belly, Nagato closed his eyes in concentration and forged ahead, “Despite the council’s gross negligence to my clan and the memory of the previous Hokage, I am willing to propose something that you will all agree to or face an uprising this very night.”
The council was quick to respond, kunai and other weapons being drawn, even Itachi activated his own Sharingan.
Nagato smiled at this, “It seems that you have underestimated the Uzumaki and Uchiha clans yet again. Did you honestly think I would come here without having insurance policies put in place?”

 

Nagato opened his eyes again, his Mangekyou Sharingan shining bright red in the light of the room, “For years now I have been in contact with Fukagu Uchiha and we have been planning for a day for the Uzumaki clan to return to Konoha as an ally of the Uchiha. Unfortunately you have forced us to move our plans forward quite a bit since you have been trying to influence Itachi into doing your dirty work. The Uchiha clan has armed and armoured everyone of Chunin rank and above and I have added a hundred of my own clan to that mix, which gives us roughly one hundred and thirty fully matured Sharingan users as well as nearly a hundred other fighters. I have also taken steps to have Naruto guarded by my men, so in short we have your precious Jinchuriki in our grasp. With these as bargaining tools I intended to negotiate with the council and have myself placed as the new Hokage or we would begin our uprising.”
Nagato could tell using his Sharingan that the council had begun to infuse their chakra, so he began to do the same as a way to intimidate them. Judging by the looks on the faces of many of the council within seconds of him infusing his chakra, it had worked splendidly.
Hiruzen was stunned, this man, this Nagato Uzumaki, was only now beginning to infuse chakra within his body and he was already at an astronomical level of power, he had power enough to give Hiruzen pause within moments of beginning to infuse his chakra.
Danzo spoke up then, a wicked smile playing upon his lips, “You do realise that the Uzumaki and Uchiha clans are still outnumbered twenty to one by the standing force of shinobi in Konoha?”

 

Nagato looked Danzo directly in the eye, his face contorting into something akin to a beast snarling, “Do you think me so foolish as to only have two clans on my side and making this move? Do you think me an idiot? I have at least seven other clans on my side and if the fighting were to quickly go in our favour, many more would join us! I’m guessing that you didn’t know that, Danzo the Sharingan thief!?”
Danzo was shocked, a look of fear upon his face, he was about to deny the accusation when Nagato stopped him by steaming ahead with his accusation, “Do you think that I cannot sense Shisui’s chakra in that right eye of yours? Who do you think taught Shisui how to unlock his visual powers to the degree that he had?! It was me! I taught that amazing young man everything that he knew and you squandered him to increase your own pathetic power. The slaughter of the Uchiha clan would have just given you access to more spare Sharingan, would it not?”

 

Danzo was silent for quite some time, the Hokage and the other elders on the council simply looking at him with accusing glares; he remained silent though and looked away from the council. His silence was akin to an admission of guilt and with his deafening silence, the council knew he could not deny Nagato’s accusations.
Nagato turned his gaze back to Hiruzen. The Hokage was looking at his old friend Danzo with disappointment and disgust in his eyes; he could no longer vouch for Danzo’s character, methods or even as a shinobi. Hiruzen looked at Nagato, careful not to look into his eyes and asked, “What are you demands?”
Nagato smiled and allowed his Sharingan to go back to their normal state, “They are similar to my original demands but with a few minor changes.”
Nagato looked at the council he could see their chakra flows with his Sharingan, they were nervous, they were unsure of how to proceed and they felt unimaginable fear when they gazed upon him. The only one in that room who did not gaze at him with abject fear was the young Uchiha sitting beside him, Itachi. He was the only one in the entire village that would give Nagato pause if they were to fight, but Nagato did not want to fight this young man with so much potential.
“Hiruzen-sama, firstly; you are to step down as Hokage and name a fifth Hokage to replace you by tomorrow at noon,” began Nagato.
“Secondly, you are to publically acknowledge the Uzumaki clan as a member clan of Konoha and return all our properties we once owned in the village.”
Hiruzen was nodding as Nagato made his demands.
“Thirdly, you are to sit with me and explain everything to Naruto about what happened to his parents the night he was born and you are to beg for the boy’s forgiveness. Fourthly, you are to hand Danzo into my custody before this evening ends and you will allow me to do as I please with him.”
Hiruzen looked at Danzo then, but his friend was merely staring at the wall next to him, his pride too strong to allow him to gaze upon the man whom was taking everything he had away from him.

 

Nagato drove on with his demands, “Finally you are to name a person of my choosing to the position of Hokage and allow both myself and Fukagu to act as personal advisors to the new Hokage.”
Hiruzen was tired, he was tired of being Hokage, he was tired of the stress and the pain it caused him and was going to name either Jiraiya or Tsunade as Hokage in a few years, but he would have to listen to this new leader of the Uzumaki clan and name someone of his choosing. He heaved a sigh and asked Nagato the fateful question, “Whom would you have me name as the new Hokage?”
Nagato smiled then, he had won this, ‘Konoha Civil War’, before a drop of blood was spilled and now he was going to give Konoha someone that would truly do anything to protect the village and its people from harm.

 

“I would like you to name,” Nagato began, a smile creeping onto his face, “Itachi Uchiha as the fifth Hokage of Konoha.”
The council was stunned, but not outraged, that was good, they might accept someone as caring for the village as Itachi as their new Hokage. They all looked at the young man who was now standing next to Nagato, the chair he occupied now on the floor, Itachi had activated his own Mangekyou Sharingan and the kunai in his right hand was at Nagato’s throat, ready to slit it if he so much as moved in a threatening way.
“What are you playing at?” asked Itachi in a barely audible whisper, confusion and frustration making the young man’s body tremble. He was crying, despite his face being a mask of indifference. Nagato activated his own Mangekyou Sharingan and turned his head to look Itachi in the eyes, man to man, Sharingan to Sharingan and heart to heart.
“Why are you doing this?” asked Itachi, his voice now quivering with emotion.

 

Nagato answered Itachi in a soft, comforting and reassuring voice, “My Mangekyou Sharingan have gifted me with foresight. I have foreseen many things with these Sharingan, things that are, things that could be and things that will be. I have looked into your future many times, since I first heard of your promotion to Jonin and to ANBU from your father. I looked at what will come if you do not move from the path that you are currently walking and all that I can see in your future is pain, unbearable and incurable pain. I watched what would have happened if you had undertaken the mission that Danzo the Sharingan thief would have given to you. He would have made you slaughter your entire clan; man, woman and child. It brought me to the verge of madness just watching what he would have made you do.” Nagato’s face was also streaming with tears now, “I may have not met you or your clan face to face, but over the last few years I have come to know you from afar, you, Sasuke, your father, mother and many others in your clan. I have grown to love them and hold them dear to my heart, not just because I share blood with you, but because you are all worthy of being loved. Itachi, you have never thought only for yourself, you have only ever thought about what you need to do to protect those you love and Konoha itself. You do not deserve the fate that Danzo and Hiruzen-sama had in store for you. A young man like you, with a heart as good and a soul as pure and kind as yours does not deserve to be disgraced and hated, you deserve to be loved, adored and admired.”

 

Itachi surprised Nagato then, the young Uchiha dropped his kunai and seemed to fall forward, but all he did was grab a hold of Nagato and hug him with all his might. Nagato, tears still wet and hot on his face stood to make the hug less awkward and held the sixteen year old tightly to his chest. Itachi sobbed into Nagato’s chest, relief and joy washing over his entire being. In Itachi’s eyes he didn’t care if Nagato was a complete stranger, he had saved Itachi from committing a heinous act of brutality.
Still holding Itachi, Nagato looked towards the council, Mangekyou Sharingan fully charged and ready for action and said in a level voice, “What you were about to make this boy do was a crime that none of you would ever have committed yourselves, but you were willing to give him the mission of destroying all that he loves in this world. You have our terms, either you accept them in the next few minutes or you can face the might of the Mangekyou Sharingan.”
Itachi had stopped sobbing, but was still in Nagato's embrace, his face buried in Nagato's chest. The tension in the room was so thick it could be cut with a knife, the council were staring Nagato down, looking for the slightest sign of weakness, but they would find none. Nagato was sure of himself and his cause; he would not allow his family to die needlessly. The council was still staring at him minutes later when Itachi had disentangled himself from Nagato and was now standing next to him as though the two of them were close family.

 

Nagato became impatient and made his decision, “Time is up, what is your answer?” He looked Hiruzen dead in the eyes ready for battle if need be.
Hiruzen answered then, “It appears that we have no choice, we will agree to your demands and…”
Unfortunately for the council, Danzo had other ideas; he had thrown the bandages covering his left eye away and was now showing off his stolen Sharingan for the world to see. He was charging at Nagato, kunai at the ready and Sharingan powered up to full strength. Itachi tensed at Nagato’s side and seemed ready for a fight. What Danzo didn’t expect was Nagato to put him under a genjustu nearly instantly, “Mangekyou Sharingan!” shouted Nagato, his eyes glowing bright with chakra as Danzo fell to his knees in front of him and dropped his kunai. Nagato knelt down to grab Danzo by the chin and force his head up.
“I take it that you agree to my terms?” asked Nagato, his eyes not leaving Danzo’s.

 

Hiruzen was the one to answer him, “Yes we do, and we do this to both strengthen and protect Konoha.”
“Good,” said Nagato a smile on his lips, but the smile suddenly died. “Now, bear witness to what happens to those that wrong the clans Uzumaki and Uchiha,” Nagato said, bringing his right hand up to Danzo’s right eye and charging his fingers with chakra. There was an ear-splitting scream from Danzo as Nagato removed the Sharingan. He stood up then, holding the Sharingan up to the light as if inspecting it and smiled,
“My student, Shisui, has been avenged.” He looked down at Danzo and focussed chakra in his eyes and said with conviction, “Amaterasu!”
Danzo screamed as he was being burned away by the black flames, his body charring and his chakra disappearing from the world, Nagato saw the council look on in horror as Danzo died in agony. He then looked at Itachi and saw that the youth was staring at the burning body of Danzo, part horror, part amazement in his eyes.
“Itachi, do you have Shisui’s left eye with you?” Nagato asked of the boy. Itachi looked bewildered for a few moments before he reached into his kunai bag and withdrew a chakra laced bottle. Inside the bottle was unmistakeably Shisui’s left Sharingan. Nagato took the bottle from Itachi and removed the Sharingan, discarding the bottle into the small amount of still burning Amaterasu on Danzo’s corpse. He looked at Itachi again, “I am now able to give you a gift of unimaginable power, a power that will, in time, make you every bit my equal and may even allow you to surpass me in the future. I will teach you everything I taught to Shisui and more, I will teach you the ways of the Sharingan and the Mangekyou Sharingan. However, in order for you to learn those powers I must fuse Shisui’s Sharingan with your own and we must do it now. I can already feel Shisui’s chakra fading in the Sharingan.”

 

Itachi looked perplexed and worried for a few seconds, “As in right now?” he asked while looking at the council.
Nagato drove on, “Yes, right here and right now, the Sharingan you possessed is already nearly drained of chakra. Let Konoha’s council bear witness to the securing of your future power.” Itachi looked at the not completely destroyed corpse of Danzo and then back at Nagato and nodded his assent.
Nagato gently took Itachi’s chin in his left hand and both of Shisui’s Sharingan in his right hand. Charging both his hand and the disembodied Sharingan with his chakra, he pushed them into Itachi’s Sharingan. The boy shook in pain for several seconds as the two sets of Sharingan fused, however, when Nagato removed his hand from Itachi's eyes he was greeted with something that he only ever saw in the mirror, an eternal Mangekyou Sharingan.

 

Nagato smiled, he now had an heir to his legacy, someone with the talent to surpass him in his use of the Eternal Mangekyou Sharingan.
“Come Itachi,” said Nagato, “we have some good news for your father and the rest of your clan.” With those words, Nagato turned to leave, Itachi following close behind him. Nagato refused to look at the council as they left, preferring to keep his eyes facing forward and his mind on the new task at hand, gathering the supporters of the coup and speading the good news.
“Itachi, take my hand,’ he said to the youth. The boy looked somewhat perplexed, but did as he was told. Nagato focussed his chakra in his Mangekyou Sharingan and said, “Kamui.” The two were sucked into a vortex that appeared before them and reappeared right in the middle of the Uchiha estate.
Itachi opened his eyes to the sight of the full might of the Uchiha clan gathered just inside the estate’s main gate, ready to charge into battle at a moment’s notice. Itachi saw his father walk towards Nagato and ask, “Did it work? Were we successful?”
“Fukagu, do you think I would be here without hostages if I had failed?” Nagato asked, sarcasm dripping from his words.
Fukagu smiled then and embraced his distant kin briefly, “Then I must have the honour of being in the new Hokage’s presence,” stated Fukagu with a smile.
Nagato looked thoughtful for a few moments, “I suppose you do have that honour, but it is not me who will be the new Hokage.” Fukagu looked somewhat perplexed at Nagato's words, however, Nagato revelling in his own shrewdness gestured towards Itachi, “Members of the Uchiha and Uzumaki clans, may I present the fifth Hokage of Konohagure, Itachi Uchiha!”

 

There was a stunned silence among the clan members for a few seconds and all eyes were on Itachi, but then a single clap broke the dam and all the people in the estate’s square erupted in applause and victorious shouts. Fukagu rushed to his son’s side and hugged him tightly, Itachi’s mother ran up to them next and eventually the young man was hoisted up onto the shoulders and arms of the crowd and being tossed into the air. All the while the crowd were chanting, louder and louder, “Itachi! Itachi! Itachi!”
Their voices were being carried into the night and waking some of the villagers with their indomitable joy and happiness. Nagato was moved to his own tears of joy as his own clansmen joined the festivities and praised Itachi simply because the Uchiha clan’s joy was so intense and infectious that they could not resist. Nagato was overjoyed himself, all the horrendous premonitions he had received thanks to his Mangekyou Sharingan and its unique abilities were fading in his mind, the path that would have led to them slowly disappearing before his mind’s eye and being replaced with something all the better.

 

Tomorrow would be a day of celebration for everyone in the Uchiha clan and all their allies, but tonight he had one other duty that he had to perform. He needed to go to his nephew and claim him as the rightful member of the Uzumaki clan that he was. Nagato’s joy died down somewhat, thinking of his beloved sister only made his heart ache and tears were brimming in his eyes. To avoid having to answer any questions and not to put a downer on the jubilance, he quietly slipped away from the crowd and the now beaming Itachi to make his way to where his nephew was being kept. It was time for him to meet the only part of his sister that he had left, a little boy who was desperate for some love and attention.