A call from the Akatsuki leader forces Hidan and Kakuzu to fall back, but in the wake of the aftermath, not everyone makes it back to Konoha alive.

Naruto successfully breaks down the crystal labyrinth with his new jutsu and he and the rest of Team Kakashi come to Kakashi, Kiba and Shino's aide, and rescue Hinata as well. Meanwhile, Kabuto, Guren, Yukimaru and Gozu head to the lake Kabuto and Yukimaru went to before. What could be in the lake that Orochimaru wants?

Yūkimaru falters and the Three-Tails injures Guren. Rinji tells Yūkimaru to suppress the beast to save her, but he is unable to do so. Guren leaves her position and protects Yūkimaru with a Crystal Style shield. Naruto goes out to find Yūkimaru, but ends up fighting the Three-Tails with Guren. Despite their efforts to defeat it, the beast overpowers the two of them, and then it proceeds to swallow them. Meanwhile, Kakashi, Shino and Sai find Yūkimaru unconcious and flee with him, leaving Kabuto frustrated.

The Sealing Team prepared to start sealing the Three-Tails and tell Sai to take Yūkimaru somewhere safe, but he gets attacked by Kabuto's men. Kabuto meanwhile prepares his plans while Lee, Tenten, and Kiba are also attacked. Rinji finds his men and converts them back to his side, ordering them to attack the Sealing Team; they're stopped by Kakashi, Yamato and Shino. Rinji then makes Yūkimaru eat the pills to control the Three-Tails, which Naruto and Guren learn about.

Orochimaru reveals the true, hideous form his body has taken from years of experimenting on his body. Can Sasuke defeat this menacing form, or does Orochimaru still have a few tricks up his sleeves?

Having successfully recruited Karin, Sasuke seeks out the final member for his platoon, Jugo. Karin warns Sasuke and Suigetsu of Jugo's uncontrollable murderous instincts, but as they arrive at the northern hideout, they find another matter they must attend to first. Elsewhere, shocking news reaches the ninja of Konoha.

Kakashi splits the two teams into five separate groups, each aided by a couple of his ninja dogs, in order to locate clues about Itachi and Sasuke's whereabouts. Unbeknownst to everyone, familiar foes have set their eyes upon both Naruto's group and Sasuke.

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.

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?

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.

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.

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.

Naruto gathers his friends and tells them that he will defeat Sasuke alone. Meanwhile, the Elders of the Leaf officially nominate Kakashi to become the next Hokage.

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.

The ship is caught in a storm and Naruto uses his shadow clones to protect the ship.After the storm, Naruto wakes up and a quarrel begins between Naruto and his Shadow clones. Soon his shadow clones revolt and take control of the ship and the crew is forced to land on a nearby island. Naruto is taken hostage by the shadow clones and they put forth their demands to him. Naruto is saved by Yamato and the others only to find that it was a dream. It was caused when a Shadow clone was released and the memories of it returned to Naruto. Naruto then realizes the worth of his clones and releases them.