In the Rain Country, Jiraiya decides to take care of three young orphans for a while. Yahiko, a spunky young boy, wants Jiraiya to train him, Konan, and Nagato to be shinobi, but it's not until he sees a strange phenomenon in Nagato that he decides to do so. What is the secret behind Nagato's Rinnengan eyes? What will become of these three children?

Having suspicions about the Nine-Tails' attack on the Hidden Leaf Village years ago, Jiraiya tells one of his frogs that the time may come when Naruto will need to access the fox's full power. His interrogations finished, Jiraiya sets out in search for Pain, but winds up encountering Konan instead. Is there a connection between Jiraiya, Konan, and the mysterious Pain? Elsewhere, one of Naruto's shadow clones runs into Team Hebi.

Itachi reveals to Sasuke that Madara is the second culprit behind the Uchiha massacre, as well as the history of the Mangekyo Sharingan and the first two Uchiha to obtain it: Madara and his brother. One question still remains: Why did Itachi really spare Sasuke's life?

As Sasuke has finally fulfilled his goal in killing Itachi and avenging his clan, he collapses from exhaustion. The news of his victory reaches the Leaf ninja and Tobi, who both race towards Sasuke's location. What does Tobi plan to do with him and who will reach Sasuke first?

Seeking to gain Sasuke's trust, Madara reveals to him the origins of Konoha. Madara and the future First Hokage founded the village long ago, but a rivalry between them would one day stem a chain of events leading to THAT night, the night that Itachi Uchiha annihilated the Uchiha Clan.

As Naruto heads back to the Tsuchigumo Clan village, Akaboshi and his group find Hotaru with the help of Hotaru's uncle. Hotaru manages to escape but the ninja bandits surround her in the forest. Utakata comes to her aid and manages to take her and escape from the ninja bandits. Akaboshi and his group are about to chase after them until their boss arrives and reveals to them that Utakata is in the Hidden Mist Village's Bingo Book.

Naruto, Sai, and Yamato arrive to save Hotaru and Utakata from the attacking ninja who they discover are Anbu from the Hidden Mist Village. Yamato attempts to negotiate alone with the head of the Mist Anbu, Tsurugi, and after their discussion, Tsurugi talks to Utakata alone. Tsurugi attempts to convince Utakata to return to the Hidden Mist Village but the latter refuses and remembers the horrible pain he suffered at the hands of his former master.

Team Kakashi returns to the Hidden Leaf Village after completing their mission. As Naruto thinks back to the talk he had with Itachi, he's summoned by Tsunade, where he discovers shocking news regarding Jiraiya.

The code Jiraiya left behind is finally deciphered, but what exactly does it mean? Meanwhile, Naruto continues his training.

Naruto succeeds in mastering his Sage Mode, taking it farther than even Jiraiya could. Things aren't looking so great for Konoha, however, as Pain prepares to make his move.

The Akatsuki Leader, Pain, begins his invasion of the Hidden Leaf Village. The Leaf ninja assemble to protect Naruto's whereabouts, but when Pain targets Iruka, Kakashi must face off against him.

Kakashi continues to fight against Pain. With the arrival of Chouji and Chouza, things start looking up, but Pain's not out of tricks just yet.

When Kakashi falls against Pain, the situation only grows worse for Konoha. Shizune and Inoichi are close to unraveling the mystery of Pain, but when the Animal and Human paths of Pain appear before them, can they escape with the truth about Pain?

Ebisu protects Konohamaru from Pain and refuses to divulge any information about Naruto. Ebisu is willing to give up his life in order to protect both Naruto and Konohamaru. Konohamaru isn't about to let his teacher throw his life away, but what can he possibly do against Pain?

Naruto returns and discovers that the village has been devastated by Pain's Shinra Tensei attack. Naruto requests that everyone stays back as he prepares to take on all six paths of Pain at once.

Naruto successfully begins taking out Pain's bodies one after another, but when his Sage Mode reaches its limit, Pain attempts to take control of the battle. Is the moment of Pain's victory at hand, or does Naruto have a plan?

Pain's God Realm finally enters the battle. As Naruto's toad allies fall one by one, the situation begins to look grim. Can Naruto defeat Pain?

The Fourth Hokage, Minato Namikaze, left behind his legacy before he passed away. Naruto, Sakura, and Sasuke attempt to find Minato's legacy before the other shinobi teams can get to it.

Naruto, Sakura, Shikamaru, Ino, and Choji continue to search for the Fourth Hokage's Legacy while chasing off some unexpected visitors.

Nagato tells Naruto about how he met Yahiko and Konan and later came to be Jiraiya's disciple.

With Nagato's story done, Naruto tells him his answer, declaring that he won't abandon the legacy of his master, and he'll keep striving for peace no matter what pain he's put through. Nagato reflects on what Naruto says, thinking back to his final days as one of Jiraiya's students. How will Nagato ultimately respond to Naruto's answer?

Deciding to believe in Naruto, Nagato uses the Gedo Art: Rinne Rebirth jutsu, expending the last of his chakra, and thus giving his life, to revive every person in the village who died in the attack, saying that it's the least he can do. With Nagato dead, Konan leaves Akatsuki, taking Nagato and Pain's God Realm (who is actually the body of Yahiko) with her, parting with Naruto saying that since Nagato believed in him to achieve true peace, she will as well. As Naruto returns to the Leaf, he is astonished to find the entire village awaiting his return, hailing him as a true hero. After all these years, Naruto has finally received the acknowledgment he's always wanted.

As chaos breaks out at the Five Kage Summit regarding Mifune's proposal to make Danzo leader of the alliance, Ao discovers something unsettling about the new Hokage. Meanwhile, Shikamaru goes to Sakura and asks permission to take decisive action against Sasuke. How will Sakura react, and what is Danzo's secret?

With Team Hawk exposed, Sasuke begins to ruthlessly take down all opposing samurai. Raikage, along with Darui and Shii, track down Sasuke. The two sides engage in battle, and Suigetsu and Juugo join the fray. Which side will win this battle of overwhelming power?

As Killer Bee's battle with Kisame rages on, the latter reveals a hidden trump card ability connected with Samehada. Meanwhile, Ao chases down Danzo, Fuu, and Torune, but they anticipate this and set a trap for him. Can Killer Bee and Ao make it through their individual clashes in one piece?

Sakura ditches her team and goes alone to Sasuke's location. Meanwhile, Madara advises Sasuke to finish off Karin, but at the last second Sakura intervenes. After so long, what interaction will take place between Sasuke and Sakura?

Naruto reproaches Sasuke for attempting to kill Sakura. Then Sasuke reveals that he killed Danzo with his own hands. He goes on to declare his intent to purify the Uchiha clan’s name by annihilating the Hidden Leaf.

The formation of the Allied Shinobi Forces is ratified by the Feudal Lords of the Five Great Nations. Each Kage returns to their village to prepare for the coming war.

In Mount Myoboku, Gerotora, Fukasaku, and the Great Lord Elder are debating whether to give Naruto the key to the Tetragram Seal left behind by Jiraiya, an act that could unleash the Nine Tails.

At Mount Myoboku, Naruto prepares to store Gerotora within himself, but hesitates as it also holds the potential risk of unleashing the Nine Tails on the world.

During their voyage, Naruto, Yamato, Gai, and Aoba stop at an island to recover from severe seasickness. There, they unexpectedly meet up with Sakura, Ino, and Choji, who are on an assignment to gather medical herbs for Tsunade.

On their way to the Land of Lightning, Naruto's ship gets caught in a storm. When the crew gets out of it, they encounter a savage group of pirates, who attempt to sink their boat and capture them. Yamato shields the boat with a Wood technique and they escape underwater in a sub-like contraption, which promptly falls apart. They wash up in an underwater cavern underneath the island the pirates had taken over some time ago. The residents of the island had taken refuge in the caves until they all died. Naruto swears to avenge them all. With a clever plan, Naruto and the ship are rocketed out of the island's dormant volcano top using underground hot springs and he successfully avenges the island folk by defeating the pirates.

Might Guy recalls their "visualization" training with Lee in order to avoid learning the Drunken Fist and forgetting an incident which Might Guy apologizes to the restaurant owner with humiliation. Lee, who is determined to train to be stronger than Naruto, follows Might Guy's orders and resemble animal fighting styles which represent on a restaurant menu. However they failed, until they tried on training on a moving boat. Like Guy who has seasickness, Lee also suffers from seasickness but he uses it to balance the boat which resembles exactly as the Drunken Fist fighting style. Guy lately realizes that Lee is also aware of the restaurant incident and Lee was only protecting Guy from a drunk man which causes the restaurant to be totally damaged.

Sixteen years ago, Fourth Hokage Minato Namikaze and his wife Kushina are expecting their first child, much to the delight of the young couple.

Kabuto and a reanimated Deidara attempt to grab hold of the jinchuriki, but are stopped by the Tsuchikage, who has come to protect Naruto.

The Allied Shinobi Forces’ commando unit engages with the Akatsuki in the first wave of battle.

The Akatsuki dispatch an army of powerful reanimated shinobi and White Zetsu across the war zone, causing chaos within the Allied Shinobi Forces’ chain of command.