Sakura reflects upon a time when she was infected with a strange disease by Naruto. In order to find a cure, an order was issued for Naruto to be quarantined at all costs before he could infect anybody else.

Naruto, two jonin and an elder known as "the Eternal Genin" set off to a mission to patrol the border of the Land of Fire following Orochimaru's attack. After some days with no incidents, a group of enemy ninjas cross the borders. The Eternal Genin proves to be a brave ninja and remembering the lessons he learned with the 2nd and 3rd hokages, sees the similarities between Naruto and his father.

As chaos breaks out at the Five Kage Summit regarding Mifune's proposal to make Danzo leader of the alliance, Ao discovers something unsettling about the new Hokage. Meanwhile, Shikamaru goes to Sakura and asks permission to take decisive action against Sasuke. How will Sakura react, and what is Danzo's secret?

Danzo brings forth a forbidden genjutsu known as Izanagi, which has the astounding power to turn dreams into reality and vice versa. Izanagi's great power comes with a time limit, but Sasuke's strength is rapidly dwindling as well. Can Sasuke resist long enough, or will Danzo completely overpower him?

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 meets two kunoichi ninja named Shizuka and Tokiwa from the Nadeshiko village who are seeking the student of Jiraiya.

Motoi confesses to Naruto and Yamato that he attempted to kill Bee during their childhood because of his father's death due to the sealing of the Eight Tails 30 years ago.

Naruto makes his entrance onto the battlefield and uses his sensory powers to detect and destroy the transformed White Zetsu clones. During the battle, Shikaku updates Naruto with what they currently know on Madara.