Asuma’s team reaches the bounty station and ambushes Hidan. Izumo and Kotetsu attack Hidan, but are unable to kill him despite stabbing his vital organs. Asuma tells his teammates that if they retreat they will be killed and Konoha will be endangered. Shikamaru realizes that Asuma is considering sacrificing himself to help defeat the enemy, based on what he knows of Asuma's shogi strategy. Asuma begins fighting Hidan, while Shikamaru distracts him by forcing him to dodge Shadow Sewing. Hidan cuts Asuma on the cheek and steps into a circle of blood as Asuma uses a jutsu to engulf Hidan in a cloud of ash. Asuma then sets the cloud ablaze, supposedly killing Hidan.

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.

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?

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.

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