In order for Kawaki to become a genin, it’s decided that he can take a special test that differs from the one held at the Ninja Academy. A D-rank mission is deemed to be equivalent, so Kawaki is assigned as an additional member. However, he is difficult to work with, ignores the need for teamwork, and acts on his own—giving his teammates a hard time while disrupting the mission!

Cho-Cho is injured in an attack by a mysterious ninja and the item that Mozuku had been holding is stolen. Captain Shikadai realizes that this was no ordinary guard mission, but one that makes them the targets of other ninja. He immediately decides to turn back toward home. But Kawaki feels for Mozuku, who was entrusted with the item that would save his people, so he ignores Shikadai's orders and pursues the ninja along with Mozuku. All alone, Kawaki faces a powerful enemy who uses a strange jutsu. Will he be able to protect Mozuku and safely return him to the Land of Calm Seas?

The new Team 7—with Kawaki its newest member—is assigned to escort Katasuke to a ceremony in the Land of Water. Boruto is looking forward to seeing Kagura Karatachi, a shinobi from the Land of Mist whom he hasn't seen since their Academy field trip to the Land of Water. However, in the shadows of the ceremony, a group harboring a grudge stealthily begins to make its move.

The Land of Water is taken over by pirates, and contact with Denki's Team 5 is lost. The new Team 7 joins up with a unit led by Kagura and sets out for Dotou Island to assist Team 5 and rescue the islanders. However, the unit is made up of Buntan, Hebiichigo, and Kyoho, who in the past had called themselves the “New Seven Ninja Swordsmen of the Mist.” Sarada and Mitsuki go ashore to scout the island while Boruto and the others stay back and watch the situation nearby.

As Sarada and the others hurry to evacuate the people of the island, Boruto grows anxious when he learns they are being threatened by the mobile fortress, which is equipped with a powerful weapon. Kagura, Hebiichigo and Kyoho show up to assist Boruto, Kawaki and Buntan. Together, they do what they can to destroy the weapon to protect their friends, but they are obstructed by Tenma and are forced to fight him.

Boruto joins Ikada as he sails to a factory where they can get a component needed for ship repair. He is impressed by Ikada’s excellent piloting abilities. Ikada reveals that he left home despite the protests of his family to look for work that involved ships. That was when he met Kajiki and found his dream of becoming a great ship carpenter. They spot a ship that has been in an accident, and while working together to save the passengers, Boruto sees something unbelievable.

In retaliation against Boruto and his friends for destroying Tenma’s mobile fortress, the pirates land on the Isle of Shipbuilders. Funamushi, a follower of the Funato Clan, attacks Kagura, hoping to capture him alive so that he can use him as a bargaining chip. Kagura fights back using the Hiramekarei—the twin swords that the Sixth Mizukage Chojuro entrusted to him—but Funamushi is a formidable foe. Meanwhile, Seiren appears before Boruto and torments him with her persistent attacks. Can Boruto find his way out of this predicament?!

As Boruto and the others ready their plan, they learn that one enemy unit is heading to the village ahead of the rest. Since they haven’t finished making preparations, the village will be in danger, so they hurry to evacuate everyone. Kagura worries that they won’t have enough people to fight. Just in case, he releases the curse placed on Buntan, Hebiichigo, and Kyoho, temporarily setting them free. Hesitantly, they agree to fight alongside Kagura and Boruto.

Despite children being present, Funamushi fights fiercely with disregard for the damage he causes. Meanwhile, Araumi is informed by his eldest son Isari that his adopted son Tenma has died in battle. With his daughter already hovering between life and death, he explodes with rage. He declares that he will be taking full command in the battles to come.

Araumi is furious about the loss of family members and many of his subordinates during the battles so far. He officially declares war against the Land of Water. Upon hearing this, Mizukage decides to fight him to the bitter end. As war between the Land of Water and the pirates becomes inevitable, Boruto is confused by Ikada’s decision to fight the Land of Water. He does everything he can to prevent any more casualties, and Sarada and Mitsuki assist him in his efforts.

Boruto, Sarada, and Mitsuki go meet with Ikada, who has now sided against the Land of Water. Boruto tries talking to Ikada as a friend to get him to stop fighting. But since Boruto is responsible for what happened to his sister Seiren, Ikada refuses to listen. Even still, Boruto persistently tries to reason with him. Ikada coldly proposes a certain condition.

Boruto and the others return safely to the Leaf Village. While Naruto informs Team 7 of events that have occurred in the Hidden Mist since they left, Boruto and Kawaki get into an argument over whether or not Ikada should be punished.

Naruto has been asked to play himself in the popular Evil Jammer Kagemasa shinobi movie series. Konohamaru ends up playing the role in his place. Since this is his first movie appearance and the fact that he will be playing the Seventh Hokage, someone he looks up to, Konohamaru goes all out. However, he’s troubled when production doesn’t quite go as he expected. Upon hearing something from the assistant director, he proposes something to make the movie more enjoyable.

Mitsuki worries when Mikazuki the cat goes missing. Mitsuki, Boruto, and Sarada are assisting with the village patrol at the request of the police department, which is having difficulty investigating a strange series of attacks. From morning until night, Mitsuki spends his days on patrol, when one day, he sees Mikazuki being cared for by another person and being called by another name!

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!

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.

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

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!