Yamato takes temporary leadership of Team Kakashi while Sai insults both Naruto and Sakura. While preparing to set off, Sai receives an envelope from a Root shinobi containing secret orders from Danzo, and Sakura consults with Tsunade. Jiraiya then meets with Tsunade and Yamato in Kakashi's hospital room to brief Yamato on the demon fox within Naruto, detailing the "demon fox's cloak", and revealing a scar he got from Naruto when the fourth tail formed. Finally the new Team Kakashi set off on their new mission, to intercept an Akatsuki spy and gather information about Sasuke.

Naruto, in the four-tailed state, begins attacking Orochimaru with incredible force, devastating the surrounding landscape and preventing Sai and Yamato's wood clone from approaching him. The majority of Orochimaru's attacks prove to be ineffective, but Naruto also fails to kill Orochimaru as he regenerates from any injuries he sustains. Meanwhile, Kabuto advances toward Sakura and Yamato, deducing that Sasori has died. Orochimaru finally manages to strike Naruto with a sword blade from his mouth, and Sakura reacts in horror when she sees Naruto's four-tailed state.

Kakashi is released from the hospital and begins Naruto's training program. Naruto learns that he has Wind-style chakra. Yamato helps by setting up the training field with his special jutsu. Naruto also learns that he can use his Multi Shadow Clone jutsu to speed up his training, since whatever the clones learn, the original user learns upon the clone's dispersal. Naruto and his mass of clones each take a leaf and attempt to slice it in half with wind chakra as the first step to creating his new jutsu.

Orochimaru's body has reached its limit and the time for the ritual has come. Sasuke has other plans, however, and seeks to target a bedridden Orochimaru.

Sasuke thinks that he's finally killed Itachi with the help of his most powerful technique, Kirin, but Itachi still has one final trick up his sleeve. Having used both Tsukiyomi and Amaterasu, Itachi calls upon the power of his third and final Mangekyo ability, Susano'o. Itachi has turned the tide of the battle against Sasuke, but the latter receives aid from an unexpected source. The battle between the Uchiha brothers is nearing its shocking conclusion!

As the fight between Sasuke and Danzo comes to a close, the latter will do whatever it takes to finish off the former. Meanwhile, Sakura and her team close in on Sasuke.

The Leaf Shinobi succeed in bringing young lord Shu into custody, placing a disguised Naruto as his double. But Tatewaki soon uncovers Naruto’s identity and surrounds the intruder with his men.

With Izanami activated, and Kabuto trapped within its infinite loop, Sasuke uses this time to question his brother about the technique. Itachi tells Sasuke about the history behind Izanami's creation as well as the Uchiha clan's use of the technique.

Kakashi becomes part of the ANBU Black Ops, an elite team of shinobi who are under the direct command of the Fourth Hokage, Minato Namikaze.

Following the aftermath of the Nine-Tails incident, many on the Leaf Council voice suspicions that the Uchiha Clan were behind this tragedy. The Uchiha are then placed under 24-hour surveillance by the ANBU, which causes further tensions to arise.

Sasuke returns to the Hidden Leaf Village seeking answers, and standing before him are First Hokage Hashirama, Second Hokage Tobirama, Third Hokage Hiruzen, and Fourth Hokage Minato, all reanimated.

Naruto and Minato combine their powers to perform a Sage Jutsu attack on Obito.