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.

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.

The ship is caught in a storm and Naruto uses his shadow clones to protect the ship.After the storm, Naruto wakes up and a quarrel begins between Naruto and his Shadow clones. Soon his shadow clones revolt and take control of the ship and the crew is forced to land on a nearby island. Naruto is taken hostage by the shadow clones and they put forth their demands to him. Naruto is saved by Yamato and the others only to find that it was a dream. It was caused when a Shadow clone was released and the memories of it returned to Naruto. Naruto then realizes the worth of his clones and releases them.

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.

Kabuto and a reanimated Deidara attempt to grab hold of the jinchuriki, but are stopped by the Tsuchikage, who has come to protect Naruto.

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.