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.

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.

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.

After hearing the news about Akatsuki's attack on the Hidden Leaf Village, Gaara worries about Naruto's well-being. He remembers a time in the past where Team 7 was assigned to help him out with a problem, and how nobody, especially Naruto, was eager to trust him. Yet, when his life was put in danger by people he had wronged, Naruto was the first to come to his rescue.