Sakura is caught by Sasori’s tactic and surrounded by a poison cloud.

Naruto loses all reason to anger and is gradually taken over by the Nine-Tailed Fox Spirit. Having been forewarned by Jiraiya, Kakashi narrowly manages to suppress the Nine-Tailed Fox.

Naruto is paired with Sai for the Buddy team of two, over his and Sakura's objections, while Sakura is assigned to support Yamato. Yamato conducts a simulation of the spy meeting with himself as the spy to gauge Naruto and Sai's abilities and teamwork. After Naruto makes a mistake when attacking Yamato, Sai immobilizes him and goes on to capture Yamato alone. Naruto is angry with Sai for not acting as a comrade would, but resolves to work together with him if doing so will help bring Sasuke back. Sai reveals to Sakura that he has no emotions, and little understanding of them. The group then prepares to head to the bridge.

Naruto's been having nightmares about the release of the Nine-Tail's power. Afterward, Kakashi informs Naruto that he has special training for him that will make him strong quickly. They are cut off by Team 10, who have also come to visit. Sai lunches with them and, trying to make friends by using nicknames, angers Sakura by calling Ino "gorgeous" after concluding that women do not like to hear how they really are.

Asuma's team returns from its mission. Team Kakashi returns to Konoha as well, with Sora replacing Sai on the team. Naruto tries to show Sora around Konoha but Sora goes his own way. Sora's insults precipitate a brawl with Kiba and Choji, with Naruto and Rock Lee joining in. Shikamaru and Asuma stop the fight. Later Asuma tells Sora he knew Sora's father, who is revealed as one of the Guardians involved in the coup attempt. He also shows Sora his chakra blade attack. Furido and the other body snatchers begin their attack on the Kohaku Clan.

The chakra of the Nine-tails rages out of control within Sora, preventing Naruto and the others from subduing him. Asuma and Kazuma resume their old battle, while Kazuma justifies his actions with his duty as a pawn to the "King" of the Fire Country. Naruto is repeatedly knocked down in his attempts to restrain Sora, and the chakra seeps into him and transforms him as well. Yamato is unable to suppress the Nine-tails' chakra in both Jinchūriki, being prevented by an unknown outside force. Sora's fourth tail emerges, causing the Nine-tails's Cloak to envelop his body. He temporarily gains his own consciousness when he witnesses Naruto stab himself in the leg and successfully prevent the original Nine-tails' Cloak from emerging.

Asuma’s fire jutsu strikes Hidan, but much to the team's surprise, Asuma is also burned. Hidan reveals his ability: By ingesting an opponent’s blood and standing in a ritual circle drawn with blood, the "curse" links him to his opponent and all damage inflicted on him is also inflicted on the opponent. Asuma rushes at Hidan but collapses after Hidan stabs himself in the leg. Shikamaru realizes Hidan needs to be in the circle for the curse to take effect, and uses his shadow possession jutsu to force Hidan to step out of it. Asuma forces himself to stand up and beheads the restrained Hidan.

When Hinata is labeled unfit as a successor, Hanabi's heart becomes bound to her destiny.

Karin is caught within the Infinite Tsukuyomi and dreams of her past. She was born into the Uzumaki Clan and has the unique ability to heal anyone who bites into her. Driven out of her village, the Hidden Grass takes her in, only to use her for this ability. Karin has no choice but to endure constant suffering in order to survive. She is later chosen to enter the Chunin Exams, where Sasuke saves her life. Karin has never forgotten what he did for her—or his smile.

Sasuke and Sakura join up with the others, but the Puppet User appears and blocks their path back to the Hidden Leaf Village. Sasuke wants to bring down the puppets and rush back to report to the Fourth Hokage, but Shikamaru and the others insist on staying and rescuing the jonin.

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.