Seeing Hinata almost die triggers Naruto’s anger and he goes into Nine Tails State. Naruto's power is enormous, but Pain releases his jutsu to seal him away. Hatred consumes Naruto as he tries to break the seal. With Naruto unable to calmly control the Nine Tails’ power, the village steadily heads toward destruction.

Itachi becomes a rogue ninja and joins the Akatsuki. He is welcomed and introduced by Pain and Orochimaru as the ex-Leaf ANBU and the man who massacred his entire clan. Itachi is paired up with a man named Juzo, and their first job together is to fulfill an assassination request in the Land of Water.

The Infinite Tsukuyomi does not affect Hashirama, Tobirama, Hiruzen and Minato because they are reanimated. Hagoromo, the Sage of the Six Paths, appears and explains to the four that Hashirama and Madara are the reincarnations of his sons Ashura and Indra. Hagoromo recounts the tale of how he founded Ninshu, the Ninja Creed, and about the lives of Ashura and Indra.

Chakra—whose energy connects this world to those beyond—allows Obito to leave Rin's side for a moment and appear in Kakashi’s inner psyche. Obito gives him his Magekyo Sharingan and leaves with a parting wish that Kakashi become the Sixth Hokage.