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.

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.

After failing to bring back Sasuke, the Leaf ninja start heading back to the Hidden Leaf Village. Tsunade, however, sends Katsuyu to inform them that the barrier of Mount Katsunagi of the Tsuchigumo Clan, which holds a powerful forbidden jutsu, is broken. While Kakashi and Team 8 head back to the Leaf Village, Team 7, lead by Yamato, must check out what events are taking place.

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.