Kawaki enrolls at the Ninja Academy and begins classes as a freshman with Himawari and the others. But it’s actually a secret mission to protect a princess from assassins. This is kept a secret because she’s come from abroad to study. Since it is a personal request from Naruto, Kawaki decides to attend the academy hesitantly, where the students are younger than him. Kawaki’s difficult school life with an unreliable teacher named Hana Kaka and his unique young classmates begins!

Kawaki has a hard time getting used to school life, but he succeeds in becoming friends with Princess Kae, the object of his guard mission. Meanwhile, Kae wants to get to know her classmates and invites them all to a tea party at her mansion. Since Kawaki has his mission and cannot let Kae out of his sight, he goes along. Despite feeling out of place at the party, Kawaki does his best to fit in, but then he senses something unusual…

Boruto, Sarada, and Mitsuki hold a special lecture at the Academy for freshmen like Kawaki and Himawari. The teacher in charge, Hana, will also speak, but unlike Boruto and his team—who have actual mission experience and flashy jutsu like the Rasengan that appeal to the students—she can only use conservative jutsu, so she feels inadequate as a teacher and becomes depressed. A mock training activity prepared by the trio causes the class to become deeply divided, and Hana struggles to bring the class together again.

After learning about the “Seven Mysteries” at the Ninja Academy, Himawari and several of her classmates decide to go investigate at night. Kae is among the participants, so Kawaki has no choice but to go along. But he learns that Kae does not believe in the Seven Wonders and is trying to create a fake phenomenon for the students who are looking forward to the expedition. Seeing Kae’s eagerness and excitement, Kawaki decides to help her until the end, but then something mysterious and unexpected occurs.

Kawaki and Himawari participate in a training session in the forest near the academy. The class is split into three-person teams and Kawaki ends up on a different team from Kae. Anxious about losing sight of Kae, Kawaki is unable to focus and ends up burdening his assigned team. Kae is lured away by a mysterious person and disappears. Fearing that she is in danger, Kawaki and Himawari rush to find her.

Osuka Kamakura is kidnapped for ransom along with Himawari. When the ringleader finds out she’s the daughter of the Hokage, he starts thinking of ways to use her to his advantage as well. Meanwhile, Kawaki does what he can to locate Himawari and Osuka with the help of Kae and Neon Asakusa

Kawaki and Himawari’s class will be putting on a play about the Legendary Sannin for the school festival. The students rehearse wearing prop headbands, but when Eiki discovers that Kawaki brought a real headband, he tries to expose Kawaki’s true identity to drive a wedge between him and Kae. Kawaki can’t afford to let Kae find out about his mission. Will he be able to prevent this from happening?!

After what appears to be an assassination attempt on Kae, Kawaki is cautious on the day of the school festival. The festival begins and everyone enjoys themselves. But when it's time for the play, a bomb suddenly goes off at the Academy.

The Academy students are at the hospital to visit Hana, who struggles to remember the day of the attack. At the Hokage's palace, Kawaki is relieved of his mission for not reporting the presence of the assassin in time.

Hana, who has recovered from her injuries, and Kawaki, who is back guarding Kae, return to class. Life at the Academy gradually goes back to normal. Meanwhile, Hana learns that about the attempt made on Kae’s life and regrets her inability to prevent it. She returns to the scene of the incident to recount what occurred.

Kawaki and Himawari’s class goes on a field trip to an uninhabited island in order to create new memories with Kae. Because of its distance from the village, there are all sorts of rumors about the island, and bizarre incidents occur, like the disappearance of the food they brought. The field trip suddenly starts to feel unsettling, but under Hana Sensei’s direction, the students try to work together to overcome these difficulties. Meanwhile, Kawaki suspects the assassin targeting Kae might be lurking nearby, so he steps up his watch.

The assassin targeting Kae has finally been revealed. Because of their previous clashes, Kawaki knows they are a powerful foe. He decides to chase after the assassin by himself to prevent putting any more students in danger. But Kawaki finds it difficult to do that without knowing where the assassin is; what’s more, his classmates desire to work together to chase down the assassin and save Kae. And so, the entire class begins their pursuit!

Kae has been taken away and Kawaki must face a dangerous assassin. Himawari acts as his partner and provides support during the battle. They try to corner the enemy with coordinated attacks, but the enemy proves to be powerful. Meanwhile, their classmates, who had entrusted Kawaki and Himawari to directly confront the assassin, take action in a desire to try to help. Will Kawaki be able to save his precious friends and accomplish his mission?