When Kakashi falls against Pain, the situation only grows worse for Konoha. Shizune and Inoichi are close to unraveling the mystery of Pain, but when the Animal and Human paths of Pain appear before them, can they escape with the truth about Pain?

Naruto successfully begins taking out Pain's bodies one after another, but when his Sage Mode reaches its limit, Pain attempts to take control of the battle. Is the moment of Pain's victory at hand, or does Naruto have a plan?

With Nagato's story done, Naruto tells him his answer, declaring that he won't abandon the legacy of his master, and he'll keep striving for peace no matter what pain he's put through. Nagato reflects on what Naruto says, thinking back to his final days as one of Jiraiya's students. How will Nagato ultimately respond to Naruto's answer?

In a flashback of Naruto and Sakura's, Team 7 is on a mission to take an ostrich called Mr. Ostrich to his home. They arrive at a village where they see a swordsman named Tsukado who has a vendetta to carry on a man named Katazu who killed his distant relative Shikazo. Tsukado fails to defeat him so Naruto decides to teach him unusual revenge lessons. Katazu has then took his brother's identity and attracted Shikazo's pursuers while Kageki and his family went into hiding. Tsukado decides not to kill him and ends their years of fighting though Kanabun wants them to keep fighting. The swordsmen, Team 7 and Mr. Ostrich chase the Kanabun Gang out of town.

A female spy, Hanare, from the Hidden Lock Village (Land of Key) is caught by ANBU pretending to be a musician. She is interrogated. However, the interrogation proves unsuccessful. Slowly, her past is revealed and so is her relationship with Kakashi. Team 7 spy on the two as they go around town, under the impression that the two are dating. After The Lock Village keeps a Leaf Village ninja hostage, they exchange Hanare for the ninja. It is then revealed that Hanare has a special ability, causing a large chase to occur. In the end, Kakashi lets Hanare free. The musician seen at the beginning entertaining Konoha ninja reminds Kakashi of Hanare which prompts the flashback.

Shikamaru remembers the time when Teams 7 and 10 joined together to flush out a band of bandits who were terrorizing a nearby village and had kidnapped the headman's granddaughter. With no assistance available from Kakashi or Asuma, Shikamaru was forced to lead the team of genin to the bandits' fort and come up with a plan to rescue the headman's granddaughter.

In Mount Myoboku, Gerotora, Fukasaku, and the Great Lord Elder are debating whether to give Naruto the key to the Tetragram Seal left behind by Jiraiya, an act that could unleash the Nine Tails.

On their way to the Land of Lightning, Naruto's ship gets caught in a storm. When the crew gets out of it, they encounter a savage group of pirates, who attempt to sink their boat and capture them. Yamato shields the boat with a Wood technique and they escape underwater in a sub-like contraption, which promptly falls apart. They wash up in an underwater cavern underneath the island the pirates had taken over some time ago. The residents of the island had taken refuge in the caves until they all died. Naruto swears to avenge them all. With a clever plan, Naruto and the ship are rocketed out of the island's dormant volcano top using underground hot springs and he successfully avenges the island folk by defeating the pirates.

Naruto finds an imposter that has been building his reputation by attempting to steal from other people while his friend is also attempting to gain a reputation by "beating" the imposter up so he builds his reputation even further and become a ninja.

During his final stop for supplies on an island in the Land of Water, Naruto runs into Akatsuchi and Kurotsuchi of the Hidden Stone, who are on an assignment to deliver a letter from the Tsuchikage addressed to the Mizukage.