Disclaimer: I do not own Naruto, it belongs to Masashi Kishimoto and (Studio) Pierrot
The Kyuubi Attack left many people suffering. They lost their loved ones and the Sandaime Hokage because of it and decided to take it out on whoever the Kyuubi's Jinchuuriki was, in this case Naruto Uzumaki, the son of their Yondaime Hokage, Minato Namikaze and of his now deceased wife, the previous Jinchuuriki, Kushina Uzumaki. In the beginning Minato was not sure whether or not he should announce his son's status, but did it out of faith in his people treating Naruto like the hero he is. Of course he expected the shoutings for Naruto's death from the villagers, but was still enraged by it. Before he could threaten them with punishments should they attempt something however one of the Shinobi Elders of the village by the name of Danzo Shimura approached him about Konoha's shinobi either joining in the future attempts on his son's life or they would not help him, either arriving to late or not at all, so he needed to be strong, which Danzo would be able to provide with his training. The Namikaze wanted to strangle the elder, knowing his methods were hardly humane, but Danzo asked if for a compromise to be made. Minato pondered about it and chose to make a deal with him. If Naruto's treatment didn't stop until his 8th birthday then he would allow it under the condition that Naruto would maintain his emotion. He would later come to regret his words, since it was almost certain that the treatment didn't get better and in fact it only got worse over the years.
He was denied good and healthy food, since it was poisoned; rotten; overcharged; dangerous objects were hidden inside of it or he wasn't given anything. The clothes he got where tattered, infested or attention catchers for assassinations attempts. He got tortured with every type of Jutsu: bone shattering, organs exploding and limbs twisted in unnatural ways through Taijutsu; he got burned, electrocuted, cut up by wind, crushed by earth and almost drowned by water Ninjutsu; he saw living hells through Genjutsu; he was bruised, cut up and stabbed with all sorts different weapons; and through all the torments he was subjected to he was always fully awake, courtesy to drugs, that also made it all more painful. His father tried the best he could, but those ignorant bigots just wouldn't stop no matter how many people he punished and he couldn't just kill the entire village, so eventually he stopped trying. He was therefore integrated into Danzo's own Anbu Division ROOT, where he would be doing all the dirty stuff, that should never become public, because it would stain the villages 'peaceful' reputation. Seven years after joining Naruto had enough and put an end to his own life in his father's office and he left a note behind. When the Hokage read the note after finding his son's body lying on the ground he couldn't help but let himself tear up. The note said:
"Hokage-sama." Minato flinched. His own son wouldn't even refer to him as his father, even in death. "I commited suicide to escape the hell that is life." the blond-haired Hokage winced again. "For years I have known about the Kyuubi sealed inside of me, but I understood that the people needed a scapegoat for the Kyuubi's actions weren't his own." so he knew about the genjutsu that controlled the Kyuubi. "They tortured me in every way possible, every time I cried they laughed about it, when I smiled they felt insulted and shouted at me, when I didn't react to it they would worsen it. They denied my existence and made it an absolute hell every time they got the chance to, but I let them do it, because the needs of the many outweigh the needs of the few and they needed it." the Hokage's was feeling more and more guilty with every sentence. 'I wish I could have done more for you, my son.'
"When I joined ROOT I thought, that I would finally get a better life, but it wasn't supposed to happen. Danzo put a seal on me, that prevented me from speaking about him like all ROOT members have, but mine was given additional functions to cause me pain, should I refuse to listen and that forced me to do what he wanted from me. Each time I didn't obey it felt like my body, my mind and my soul were torn apart and when I showed the will to fight the seal he would strengthen it. Then he forced me to kill my brothers-in-arms to harden my heart and when I wouldn't do it he forced them to attack me. I have eventually decided to stop resisting and just obeyed, even if I didn't want to it. On the missions he assigned me I fell in love and made bonds. I fell in love and befriended many, I gained attachments I always wished and hoped for, but all of them were taken from me, I was force to kill them, break their hearts and cause pain to them for Danzo, who I thought at the time was doing what was necessary for Konoha, I quickly realized that his actions were never for the good of the world or Konoha, it was all just for himself. I murdered countless people that many would deem innocent and I raped and broke many people on his behalf. I tortured them, both physically and mentally and crushed their minds. Among those people were people from all over the world, from every country and every village, Konoha included. Civilians and shinobi alike were taken everything, whole civilizations and cultures,everything and effectively erased just because Danzo deemed them a threat to himself. Many begged for their lives or wanted me to end their misfortune, but Danzo would not let me, he made me prolong their suffering, suffering I caused and all I could do watch it, I was a slave in my own mind, created to satisfy the pleasures of a madman." Minato gained an enraged look that screamed murder. 'DANZO! You will the day you were born. You will pay for everything you have done with your life.'
"I could've ended my life long ago, despite the seal I was not unable to, because he didn't have any means preventing it. I wanted to find a way to change the world, Danzo knew and counted on it, knowing I couldn't do it, if I were dead. I have infiltrated many countries and organizations and gained insight into the happenings of the world. The shinobi system brought order to the world, but it was pointless, because this order only resulted in more misery. Every shinobi village has been behind many cruel and inhumane actions, grudges were formed and wars started for petty reasons that should never have resulted in anything more than a simple brawl, yet conflict always arises with the most pitiful excuses. Small actions evolve into great conflicts and then full blown wars. And despite all of the atrocities the other nations have commited, I can without a doubt say that Konoha is not the peace-loving place it pretends to be. No, in fact it is by far the worst of them all, starting the most conflicts with the most brutal and most merciless approach, while keeping up the face of a paradise. It has brought anguish to far more people than it saved and inflicted far more damage than it avoided with its so-called good deeds. I would rather die with disgrace than live in a world where the real monsters like Danzo are allowed to roam free, spreading like a plague and bringing about the downfall of his own kind. Goodbye Hokage-sama, may we meet again in the afterlife." Minato couldn't hold the tears anymore and let them fall freely. 'Why did my son have to be used like that? why is this world so cruel?'
After Minato had finished reading he cleared his mind and thought about everything that was written down in his son's last message and how to proceed. He first had to make sure that everything in it was the truth and although it did pain him he had a Yamanaka, specifically Inoichi, the clan head enter Naruto's mind before it was no longer accessible and what he found out sickened him to him core. Everything that Naruto wrote was actually the sugarcoated version, since he didn't go into details and now that he had proof of Danzo's actions, which would make even the most hardened veterans throw up and even the someone like Orochimaru shiver, he was going to make an example out of him. He exposed all of Danzo's secrets and had him publicly executed, while going on a hunt for the most guilty among the citizens, two of which were the other shinobi elders. All in all Konoha suffered greatly from Minato's 'purge' and he also had everything prepared to have all of Konoha's darkest activities published or better yet discreetly sent to each nation's leaders, in case of the village becoming even worse. One wrong step and Konoha would be crushed by the whole world wanting to annihilate it for its sins, he made sure of that. And it did happen, the village pushed his hand and in the aftermath there was only a big crater left. They were utterly defeated and no one was able to escape the wrath of all countries combined, it was a massacre that made the Uchiha Massacre pale in comparison. Anyone with a Konoha headband on that wasn't present during the invasion would never be able to live in peace with everyone hunting them down, so they all committed suicide afterwards.