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?

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.

The Akatsuki dispatch an army of powerful reanimated shinobi and White Zetsu across the war zone, causing chaos within the Allied Shinobi Forces’ chain of command.

The Allied Shinobi Forces are on the verge of winning the war when Madara Uchiha appears. Madara summons the giant Gedo Statue and unleashes its devastating power.

Fourth Raikage Ay attacks Naruto in an attempt to prevent the Jinchuriki from falling into Madara’s hands. Ay is unwilling to listen to either Tsunade or Killer Bee’s pleas to change his mind.

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.

The weather-controlling enemy is revealed to be Yota, a boy who came to the Leaf Village years ago and befriended the local kids, including Naruto.