As Naruto predicted, it all happened a few days later. Shisui was sent on an emergency solo carrier mission to deliver a scroll and bring back the response as soon as possible. It was all to ensure he wouldn't be able to fight back.
Danzo picked the agents for this mission himself. He also wanted Naruto to be the one to deal the finishing blow. Of course, Naruto couldn't be more happy. The attack was coordinated perfectly. The first group of agents were to just wear Shisui down. Then Danzo would grab an eye before having Naruto kill Shisui and grab the other.
And it all went according to plan. Shisui was panting and bleeding from multiple wounds. He was being held immobilized by several agents. There was no escape. Danzo took it as his signal to enter the clearing, followed very close behind by Naruto.
Danzo gave an entire speech about the good of the village, he reached a hand to grab an eye, but mere centimeters away, he froze. Shisui, who had his eyes closed in a last-ditch effort to protect them, opened them again to see Danzo wrapped in crimson chains with multiple seals attached to them.
Suddenly the agents holding Shisui let go before moving away a safe distance. Shisui slowly raised up to see Naruto behind Danzo with chains coming out of his chest.
"What the hell?" was all Shisui could manage.
"I'm sorry for not warning you before, Shisui, but we couldn't let Danzo get away. I will explain everything. My clone already told Hokage-sama to call for an emergency meeting. We should head there." Naruto said.
His seals and chains were holding Danzo in such a way he couldn't even use a speck of chakra or make the slightest movements. There was no escape for the bastard this time.
They reached the meeting room soon enough. Shisui was on edge, but he trusted Naruto. Meanwhile, Naruto was the epitome of calmness. They opened the door, and there were various shocked reactions. Shisui immediately moved to stay to the side. The clan heads were all there, plus the Hokage, the sannin, and Itachi.
"I am sorry to call for everyone so late, but this matter simply could not wait," Naruto said.
"What is the meaning of this? Why are you treating a respectable elder in such a way?" Hiashi asked, irritated.
"I understand your frustration Hyuga-sama. In the next few minutes, everything will be revealed. We are here to set the appropriate punishment for Danzo Shimura. May I ask Orochimaru-sama to present the first set of evidence?" Naruto asked, and when Minato nodded, they moved forward.
It was evident that no one knew what was going to happen, but they had to act professionally. Orochimaru then unsealed a massive binder on the table, and it all started.
It was a long process. Orochimaru first provided all documents and evidence of Danzo's criminal actions in wars. Every shinobi he got killed to further his agenda, every illegal deal, and everything in between. By the end of it, the clan heads were solemn, but they were holding their tongues before all evidence was provided.
Then Tsunade moved forward. By using the birth certificates and documents Naruto provided, she provided evidence of all the children stolen from civilian and shinobi families and orphanages.
Then Orochimaru moved back again to tell them about all the illegal experimentations. Then Jiraiya told everyone about the seal put on agents' tongues and how they were all monitored so they could never utter a word about Danzo's actions.
So much more was revealed. Naruto wanted everyone to know of all the crimes committed in the name of Konoha. But finally, everything was revealed.
For once, no one wanted to argue or felt the urge to input their opinion; it was clear what needed to be done.
"I know all the evidence so far is enough to make a decision, but one crime was left for last, and that is the crimes against the Senju and the Uchiha clans," Naruto said as he summoned another chain to rip all the clothing off Danzo's upper body, including his eye bandage.
Everyone gasped when they saw the Mokuton arm and sharingan eyes. Fugaku looked ready to rip Danzo apart.
"After Tsunade-sama removes the arm and sharingans, I will remove my chains since my seals will ensure that he will not be able to escape. The seals can't be removed, and I wanted the pleasure of killing him to go to people who deserve it. He is able to feel, hear and see everything going on now, but he won't be able to show any reactions. He is trapped in his body."
"I am sorry I was not able to put a stop to his crimes sooner. He had so many contingency plans ready. If I made a single wrong move, we wouldn't be able to fully stop the ROOT." Naruto said.
"Wait, what do you mean?" Minato asked.
Suddenly a barrier went up around the room. "I have to inform you all that I am merely a shadow clone here to deliver a message. I've been planning this moment for a few years now. By now, I have enough control and influence in ROOT to pull this off."
"Danzo has been controlling the ROOT for years. The layers of his plans are beyond a simple explanation. Currently, the original me is putting together all the documents that fully explain things in detail, but if I have to give a short explanation, it would be that the control over ROOT is absolute."
"There is always an absolute leader. All the branded agents will be carriers of his will. It will eat away at their souls and hearts, making the will of the leader their sole purpose. No matter how much they try to resist it, with time, they will become mere puppets."
"There is no escape for them. They are forever bound to serve a master. In the past years, I slowly gained more power and managed to make it so that I would become the leader after Danzo. This seal cannot be broken, however. If there is a person chosen by the previous leader as the new one, it will carry on."
"I will make sure that the seal will end, however. But before that, all who are beyond rescue will be eliminated. Every agent who is willing to live and find a new purpose will be here by the end of the week." Naruto said.
"Wait. I thought you said that the seal cannot be broken." Shikaku said.
"Yes, Shikaku-sama. However, as the next official owner of the seal, I do not plan to appoint anyone as the next leader, and I will free all the agents before they can become a puppet." Naruto said, and the implications of what he said were not lost on anyone.
"No. You can't do this." Minato yelled as he tried to hiraishin out to no avail.
"I am sorry, but this is the only option. I only told you of one of the reasons, but I can assure you there is so much else going on. The only end for the ROOT is for the leader to die without appointing a successor. There is also the fact of the daimyo. He will find out about Danzo's actions, and he will order the elimination of those involved."
"By taking action now, we will evade his wrath. He would only find out about the betrayal and know that those involved with ROOT directly and in power are dead. He won't care about the remaining agents since eliminating all agents will put a dent in our military power. this is the only way to satisfy him." Naruto said.
The room blew into motion. Everyone was trying to find a way out. Itachi and Shisui were trying to pry open the door, and Fugaku and Hiashi were trying to use their dojutsus to find a weak spot. Shikaku came to Naruto's side.
"Please, Naruto-kun. This is not the way. You need to put down the barrier." He said, worry evident in his voice.
"I am sorry Shikaku-sama. Even if I wanted to, I am not the one holding the barrier. My only job here is keeping Danzo and answering what I can." Naruto said. Tsunade was already at work removing the limbs.
"He is telling the truth. The seal is a timed seal. It will only go down when the timer is done. I can't even use summoning to ask for help. We are completely cut off from the outside." Jiraiya said from his place near the middle of the room, inspecting the seal on the ground with Orochimaru.
"You can't do this Naruto. there must be another way." Shisui pleaded.
"Unfortunately, there isn't. I've been researching for as long as I remember. There are so many layers. If even one is not done right, the whole plan will blow up, and there will be no more chances to stop them. They deserve happiness and freedom as well." Naruto said.
"But what about your happiness?" Itachi asked.
"I loved all the time I got to spend with my friends. It made me so happy. But people in ROOT are also my friends and family. I grew up with them and fought alongside them. If I can give them their only chance of freedom, it's not even a choice to make." Naruto said.
"Please, Naruto. I can't lose you too." Minato said, tears running down his cheeks. Just then, Tsunade finished her procedure, and Naruto retracted his chains.
"Thank you, everyone, for everything you did for me in all these years," Naruto said with a sad smile before the clone popped.
A few hours later, a tiny lifeless body was found in the ROOT headquarters in the main office. A sword was lodged into his heart, and a peaceful expression was on his face.
There were many bodies all over the base, and even more, bodies were found in the next few days. The funeral was grander than anyone thought. There were so many lives the small boy changed in his time. And they all wanted to pay their respects.
Those who were closer to him were all crying. There was no use holding back tears when there was such heavy rain.
Miles away in a dark room, a boy jolted awake from his sleep in unimaginable pain. He tossed and turned, trying to keep himself from screaming. Finally, after what felt like forever, the pain subsided. The boy dragged himself to the bathroom to splash water on his face.
He looked at himself in the mirror. There were definitely changes to his appearance. He didn't care much for now, so he decided to go back and lay in bed.
It all started years ago when he first came to Uzushio. He knew that he wanted to make a safe haven in the ruins. For all of those who sought a home. But Naruto still had duties to perform in Konoha. Things that needed taking care of.
So he used a forbidden seal. Uzumakis were obsessed with the concept of Yin and Yang. Chaos and harmony. All things contradictory yet needed to complete each other. There was a seal that had a high price.
The seal would separate the person's very own soul and being into two. No one ever survived the amount of chakra needed and the strain that it put on the person, but Naruto was used to breaking the rules of nature.
He separated himself into two. So one would go back to Konoha and take care of all preparations needed while he would take care of other aspects. He forfeited his right to the name Naruto, and he took the name Yurei. Because that was what he was. A ghost.
Now that Naruto was done with his part by ending his life, all his memories and experiences were returned to Yurei. All his spy clones were also gone and done with their tasks.
There was no need for them anymore. It was time for Yurei to take the last steps.
But for now, he needed a little rest. Being separated for so long had its toll on his body and mind. They were literally two separate entities. Naruto was the light and hopeful side. The one who still had childhood wonder.
The one who was free to be a child and enjoy the love around him. They both knew of the final plan, so Naruto wanted to give Yurei a gift for taking on the more challenging task. Naruto made sure to make as many good memories as he could. To spend time with his loved ones. To be loved.
And now Yurei was able to feel all those feelings and memories. He was grateful. For years he was in the shadows. Taking actions and making decisions in secret. He wasn't alone, but he had to let go of emotions and anything that could hold him back.
He needed to do what was necessary to ensure a lasting peace. And now that he could see and feel all the years of happiness brought to his friends, he knew it was worth it. He wouldn't let his friends go through all the pain and loss the same way he did.
Yurei decided to rest for a little while before going through the last of his sealed memories. It was time to move forward.