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.

Hanabi adores her sister Hinata, who struggles to become a worthy successor to the Hyuga Clan.

Tsunade continues to read Jiraiya’s novel. Chunin- and jonin-level ninja have gone missing, and the Fourth Hokage, Minato, orders a search mission with teams of genin led by Guy and Kurenai. Kakashi’s Team 7 is also dispatched, but the hero Naruto Uzumaki, despite being the Hokage’s son, has the misfortune of being labeled a loser.

Sasuke takes his frustrations out on Naruto and the two begin to fight, this time with their respective new jutsu. Minato steps in just before it turns into a disaster. From this encounter, Sasuke realizes that he is nowhere equal to Naruto in strength and joins the Leaf Police Force, determined to beat him one day.

Upon graduating from the Academy, Itachi becomes a genin and joins a team that includes Tenma, Shinko, and their Jonin Leader, Minazuki Sensei. They accept a mission from Granny Cat to look for a missing feline who's a skilled Ninja Cat!

Hagoromo's two sons, Ashura and Indra, share a happy childhood, training and playing together. Indra is naturally gifted with great talent, and at a tender age is nicknamed the “genius of Ninshu.” On the other hand, Ashura has no aptitude for Ninshu. Still, the two boys are very close. But Hagoromo is unaware of the malevolent power stirring in the shadows…

The Tsuchikage and Raikage, who are in the Leaf Village to attend the Five Kage Summit, mention that they have already prepared wedding gifts for Naruto. Gaara finds himself in a dilemma. He's advised that the gift should be something that befits the Kazekage. He also learns that the Raikage is planning to perform a dance. Kankuro chimes in and suggests Gaara should dance as well—further plunging Gaara into indecision.