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 finally makes sense of the destruction he witnessed around him earlier. Yamato tells Naruto not to rely on the demon because Naruto is strong enough to withstand the demon's terrible chakra. Sai discovers the loss of his book while resting. Team Kakashi browse Sai's book, and they notice that the book (which can be read from both ends) contains different paths of two boys who meet in the middle. Each page has the boys fighting someone new, each time collecting the opponent's armor and weapons into the next page. The pages where the two boys would meet are unfinished. Orochimaru's group reach their base, not realizing that Yamato's wood clone trailed them there. Sai gets a glimpse of Sasuke's silhouette and eyes and discovers that he is the man Naruto and Sakura are looking for.

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.

Hidan falls into Shikamaru's trap, but now that he has Hidan cornered, can he find a way to defeat Hidan's immortality? Elsewhere, things are looking grim for Kakashi, Choji, and Ino as they continue fighting Kakuzu, but a surprise back-up unit arrives on the scene to provide some much needed assistance.

While Naruto continues practicing a combo attack with Gamatatsu, Kakashi, Kiba, Hinata, and Shino have a run-in with Guren's gang. Will Kakashi and Team 8 be able to defeat these strange foes?

After Shino finishes preparing his insects, he goes against Guren's crystal style. Elsewhere, while Shizune, Sakura, Ino and Hinata are bringing the sealing barrier to the Sanbi, they are being watched by Tobi and Rinji.

The battle for the Sanbi comes to an end as neither the Konoha ninja nor Orochimaru are successful at obtaining it. Tsunade classifies the mission of catching the Sanbi as a failure, for it is too dangerous to accomplish. As Naruto and the others prepare to return home, Yukimaru goes missing. Unbeknownst to everyone, Akatsuki lies in wait, and they have their own plans for the Sanbi.

Over ten years ago, the Five Great Nations’ were in the midst of the Third Great Ninja War. Future Fourth Hokage Minato Namikaze assigns young Kakashi, Obito of the Uchiha clan, and Rin, on a mission to Kannabi Bridge...

In the Rain Country, Jiraiya decides to take care of three young orphans for a while. Yahiko, a spunky young boy, wants Jiraiya to train him, Konan, and Nagato to be shinobi, but it's not until he sees a strange phenomenon in Nagato that he decides to do so. What is the secret behind Nagato's Rinnengan eyes? What will become of these three children?

Itachi reveals to Sasuke that Madara is the second culprit behind the Uchiha massacre, as well as the history of the Mangekyo Sharingan and the first two Uchiha to obtain it: Madara and his brother. One question still remains: Why did Itachi really spare Sasuke's life?

Naruto, Sai, and Yamato escort Hotaru to the hidden village of the Tsuchigumo Clan. Upon arriving, however, the villagers don't seem so happy to see Hotaru. Elsewhere, after Utakata reflects upon the time he spent with her, he comes face to face with Akaboshi and his group.