After a difficult battle on the home field of Konoha, many lives were claimed, and the battle was fought with all the Fire country had. Upon entering Konoha, Nagato, utilizing his six other bodies from a distance, along with Konan, invaded the village. Those lost in the battle included Shizune, Akimichi Chouza, and many more fine Konoha shinobi. Naruto, unfinished with his training in Myoubokuzan, returned to Konoha as soon as the messenger frog arrived. Thanks to him, Hatake Kakashi, Tsunade, Team Gai, Team Kurenai, the former Team Asuma, and others, Konoha managed to defeat the bodies of Pein. Kakashi and Naruto found and chased after the real Nagato and were soon joined by Sai and Sakura. Eventually a battle broke out between the real Nagato and the Neo-Team Kakashi. However, as the team from Konoha was more than a little fatigued from fighting the six bodies of Pein, Nagato had the upper hand. But, the Sand Siblings arrived just in time to back up the team from Konoha, and soon Nagato was brought to his knees and near death. Upon seeing the Deva Realm Pein's body, the body of Yahiko, Nagato's childhood best friend, dead several yards from him, Nagato saw the error in his ways and remembered the times he shared with Yahiko. Crying and hoping he could join his friend wherever he was, Nagato died, and the battle was finally over. Konan, who escaped back to Amegakure after Pein's defeat, reported what happened to Madara, Kisame, Zetsu, and Team Hawk. Madara never thought that the strongest of his Akatsuki would be taken out like that, but he knew that Konoha was now severely weakened. He was confident, for he had Sasuke to aid him as well, or so he thought. Madara informed Team Hawk and Konan they would immediately be heading for Konoha.

Meanwhile, the message from the Raikage had been sent to the five Kages, and not long afterward, they all gathered together. They knew they had to stop Akatsuki as soon as possible, and it just so happened that one of them knew of a sealing jutsu that could stop Madara for good, but it required a very large amount of chakra (far beyond that of any one or two people). He proposed that the five of them settle their differences and work together to stop this threat. After a bit of hesitation, all five eventually agreed and so the stage was set.

When Madara, Team Hawk, and Konan returned to Konoha, they found most of the villagers attempting to rebuild some of what had been destroyed. Madara, thinking he had the upper hand, was caught off-guard when Pa Toad shot out oil onto Konan from behind, upon which Mitarashi Anko shot out a fire jutsu and lit her aflame. Kakashi then finished her off with a Raikiri in one swift move. Madara ordered Team Hawk to destroy these opponents quickly, but they refused to comply. Karin, Juugo, and Suigetsu said that they would only follow Sasuke and he had decided that now was the time to fight back against Madara. Sasuke activated his special Mangekyou Sharingan and used the flames of Amaterasu on Madara's chest as quickly as possible. Madara dispatched the black flames with apparent ease, but Naruto quickly came in with a Fuuton: Rasengan to attempt to strike Madara again while he was distracted by Sasuke's revolt. However, the attack passed right through Madara, just as one of Naruto's previous Rasengans had, before even the death of Itachi. Kakashi, activating his Mangekyou Sharingan, tried to use Kamui on him, but it had barely any effect on him. Still, it did stop him from using his own secret jutsu. Right then, the 5 Kages emerged from the ground and each put their right hand on Madara and, using the sealing jutsu, put forth their chakra, which eventually sealed Madara as a statue of diamond. This statue happened to be made out of the same material as the First Hokage's necklace, which Naruto still has with him now.

This epic battle ended Akatsuki permanently, as Zetsu and Kisame ran off and went into hiding. Sasuke, Juugo and Karin joined Konoha, and were welcomed warily by Tsunade. They had helped against Madara at the end, but she was still not sure that she had their full allegiance. As for Suigetsu, he set off on his own to capture the rest of the Seven Swords of the Mist.

Peace returned as the ninja of Konoha once again began rebuilding their village. A problem arose though: who would guard Madara's statue? The Kages argued strongly, since keeping Madara's statue would be a big responsibility to prevent him from ever coming back. Sunagakure was eventually chosen to watch over the statue. The Tsuchikage though, being an opportunistic man, found Konoha being weak as an opportunity to strike it down, revenge against the Fire Country from the last ninja war. Sunagakure found it unfair that they were given the huge responsibility to guard the statue, but the Kazekage, Gaara, pleaded with the village to have faith and be patient, as right now the main mission was to restore peace to the world.

However, this obviously wasn't the mission of the Tsuchikage. He sent select Iwagakure shinobi to kidnap Hyuuga Hanabi and to leave a Kumogakure headband. As there was a past incident where a Kumogakure ninja had tried to kidnap Hyuuga Hinata for the secrets of the Byakugan, Konohagakure had no doubt that Kumogakure was indeed behind it and demanded that Kumogakure return Hanabi or face the consequences. But, Hyuuga Neiji wasn't certain that Kumogakure had done it. He was well aware of the past incident as it had cost him his father, but he was suspicious of Iwagakure, who was being uncharacteristically helpful to Konoha in demanding the return of Hanabi. He urged Tsunade to allow him and his team to investigate until she reluctantly agreed, but warned them to keep their presence a secret. Team Gai then went off to Iwagakure to investigate, but unfortunately they were discovered in the middle of their investigation. The Tsuchikage, acting innocent, threatened war against Konoha if they did not withdraw their shinobi and if they ever tried to investigate something within the borders of Iwagakure without his permission again. Tensions were high and it was then that Hanabi managed to escape her confinement and make herself visible to Neiji's Byakugan. After he told Tsunade, she angrily declared war on Iwagakure. And just like that, the 4th Great Shinobi War had begun.

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Five years have passed since the defeat of Akatsuki and the beginning of the war. The war is still going, with both sides claiming heavy casualties, but Konoha is mostly rebuilt now and is starting to get a bit stronger again with the help of Sunagakure. Though, the war still does not seem to be going one way or the other. However, something dark is also brewing within Kirigakure. A Kirigakure shinobi by the name of Teion Genshido learned, from a mysterious stranger that remains in the shadows, the whereabouts and identity of a certain former Mizukage. Though Genshido doesn't know it, this mysterious benefactor of knowledge is none other than Zetsu, formerly of Akatsuki. Genshido had recently stumbled on a lost scroll containing information on a secret army and its leader, Sojobo, the great Daitengu. The stranger told him that Madara, the former Mizukage, is the only one who knows where the statue of Sojobo is and how to free him so that they may battle and the victor may gain control of his army of Tengu. Genshido has gathered up a band of five extremely powerful criminals, rivaling the former power of Akatsuki, along with himself and the mysterious benefactor. Their ultimate goal is to revive Madara and Sojobo to gain control of the greatest army in history. Will they succeed in bringing Madara back into the world? Will Madara and them be enough to defeat Sojobo in the end, or will he be allowed to run rampant in the world? How will the 4th Great Shinobi War end? And can Naruto and his friends hope to stop all of this madness before darkness consumes the world?!