Asuma mourns Chiriku's death, and realizes that Hidan and Kakuzu are trying to claim the bounty on his head. Meanwhile, Hidan and Kakuzu take Chiriku in for their payment. Meanwhile, Kakashi shows Naruto what the true goal of his training will be.

As Naruto recovers from his injury, Kakashi prepares to tell him the grim news about his new technique. Meanwhile, Sasuke secretly trains and has an encounter with a strange young girl.

In Konoha, Tsunade discovers they have an enemy using Crystal Style. While on his mission with Team Kakashi, Naruto meets Yūkimaru once again and talks to him. Guren puts a gigantic Crystal Prison over the forest trapping Team Kurenai inside. Guren then prepares six Crystal Clones and attacks Team Kurenai with them. Hinata defeats one clone but is locked up in a Crystal Prison by another. Team Kakashi reaches the borders of the giant prison and Naruto uses his new Jutsu with Gamatatsu to bust a way in.

Kabuto plans on breaking Leaf’s The Four-Corner Sealing Barrier from the inside by using Yukimaru’s power and have the Three-Tailed Beast go on a rampage.

The sealing team continue their efforts to seal the Sanbi while Kakashi and the others face against a monster fused together by Kigiri, Nurari and Kihou. Kabuto reveals Orochimaru's plans involving the Sanbi and he and Naruto begin to fight. While protecting Yukimaru, Guren fights against the real Rinji, who has been resurrected by Kabuto. When Guren sacrifices her life to save Yukimaru, Yukimaru's powers go into full effect. Now, in order to protect Yukimaru, Naruto prepares to go against the rampaging Sanbi.

By using himself as an explosive, Deidara creates an explosion ten kilometers in diameter, something not even Sasuke will be able to escape from. Is this the end of Sasuke? Elsewhere, someone approaches the Akatsuki leader and gives him orders to catch Naruto himself. Who is this true mastermind of the Akatsuki plot lurking in the shadows?

While the members of Team Hebi head towards Itachi's location, Jiraiya infiltrates the Hidden Rain Village in hopes of gathering information on the Akatsuki leader. Jiraiya captures two Rain ninja and interrogates them about Pain, but what he learns shocks even him.

After successfully breaking out of Itachi's Tsukiyomi, Sasuke gains the upper hand on his weakened brother. With no other alternative, Itachi activates his second Mangekyo ability, Amaterasu, a black flame said to burn forever.

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

As the ninja of the Hidden Leaf Village work on repairing their village in the aftermath of Pain's invasion, Naruto and Sakura come across a familiar face among the carpenters: Inari and Tazuna have arrived to help out. Inari recalls what happened after Gato's death and how Naruto and Sasuke came to his rescue.

During the two-and-a-half-year time period in which Naruto was training under Jiraiya, the latter decided that it was time for Naruto to learn how to repel genjutsu. During this training session, the two traveled to a village which Jiraiya had previously been associated with, but they discovered that something dark was amidst.

Naruto and Sakura learn that Danzo has been made Hokage and that his first order is to eliminate Sasuke. The two go to Sai and inquire about Danzo, but Sai reveals that a curse mark given to all members of the Foundation prevent him from revealing anything about the new Hokage. Soon afterward, Karui and Darui attack them, demanding information about Sasuke.

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.