Boruto and Kawaki join Naruto, Hinata, and Himawari on a family trip to the hot springs. The five have fun playing table tennis and enjoying the food and hot spring at the inn. Kawaki had been hesitant before the trip, not wanting to intrude, but he finds himself enjoying the time with Boruto and others. When he and Boruto learn that the inn is hosting an event which promises a premium gift, they decide to sign up and participate.

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!

While strolling through the village, Kakashi and Boruto come across some people arguing. Boruto sees a gloomy-faced young couple and learns they’re engaged, and that their grandfathers are feuding. For the sake of their future, Boruto wants to help them out and asks Kakashi for advice, but Kakashi is totally uninterested. However, something seems to sway Kakashi and he decides to help…

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?

Boruto accompanies Sasuke to a hawk trainer to obtain a messenger hawk.

There, Boruto and Sasuke hear about a person who sells rare animals and decide to investigate. Boruto then befriends a boy named Tsuzura Shitakiri. Because of his mother, Tsuzura doesn’t go to school and has given up on the things he really wants to do. His only friend is a hawk that is unable to fly due to an injury. He takes good care of this hawk in the hope that it can soar the skies once again.

Tsuzura’s hawk has suddenly been sold, so he does what he can to get his precious bird back. Hearing what happened, Boruto ignores Sasuke and rushes to help.

Boruto dozes off on Thunder Train and wakes up in an unfamiliar location along with the other passengers. A mysterious individual known as Ouga forces them to participate in a game of death disguised as an experiment—who will successfully beat this game and make it out alive?!

As test subjects drop off one by one, Boruto tries to find a way to get everyone out alive. The next experiment is for the subjects to carry candles that are directly linked to their lives. Although some people try to save only themselves, Boruto and a fellow ninja from the Leaf Village, Kiseru Gankubi, aim to clear the challenge together with everyone…but Ouga’s experiment mercilessly pushes them to their limits!

While everyone is exhausted from Ouga’s experiments, a test subject talks about their goals, which leads everyone to talk about what they want to do if they survive. The mood is lightened, but Ouga begins a new experiment. Due to the careless actions of certain test subjects, everyone's lives are in danger once again.

While Boruto and the others are forced to participate in Ouga’s experiments, Sarada and her team investigate Boruto’s disappearance and discover the existence of a suspicious individual.

Meanwhile, Boruto is shocked to discover the identity of someone who may be working for Ouga. Just then, a test subject is found dead—killed for reasons that have nothing to do with the experiment.

Ignoring the danger to his own life, Boruto tells the other test subjects to escape while he takes on the person who may be working for Ouga. But they decide to stay and help Boruto fight the suspect.

As they search for Boruto’s whereabouts, Sarada and her team find themselves surrounded by skilled ninja and uncover unexpected information about the incident.

Boruto reawakens to find he’s back where he first found himself.

Naruto falls ill, and Sasuke goes to the Tatar Observatory to try to find a cure.

Sasuke is attacked by Meno, the guardian of the Observatory, and then poisoned. Just when he thinks it’s all over, he is rescued by Sakura, who has infiltrated the Observatory as a doctor. She gets Sasuke reassigned to assist her, and they begin their undercover investigation. From the intel that Sakura brings, they learn that Ultra Particles were what cured the Sage of the Six Paths, but in order to find out where it is located, they need to obtain a document called the Map of the Heavens. They decide to search the Observatory’s library for it.

Seeking information related to the Ultra Particles, Sasuke searches the cellar of the room belonging to Zansul, the director of the Observatory, while a messenger of the prime minister is visiting from the capital. To buy some time, Sakura transforms into the messenger. While Zansul is distracted, Sasuke tries to sneak into the basement, but they start to get anxious when things don’t go according to plan. Meanwhile, Zansul tells Sakura something disturbing.

Sasuke and Sakura work together to gather information concerning the Ultra Particles. Unfortunately, there is still much they don’t know, and they are unable to figure out where to get answers. Eventually, Sasuke finds a clue to the whereabouts of the Ultra Particles from something his cellmate mentions. Meanwhile, Sakura discovers a hint to unraveling the mystery of the Map of the Heavens from a game called Star Lines. Having finally gathered the information they need, Sasuke and Sakura try to obtain the Ultra Particles. However…

A swarm of dragon-beasts suddenly appears at the Observatory, throwing everything into chaos. When Sasuke and Sakura learn that the director, Zansul, has horrifying ambitions, they split up to try to stop him. Sakura gets back to the Observatory first, but the building collapses while she’s still inside. Meanwhile, Sasuke catches sight of Zansul and his accomplices. He tries to join up with Sakura but is unable to find her. Trapped, Sakura faces a precarious dilemma.

Will Sasuke and Sakura—the most powerful couple in the Village Hidden in the Leaves—be able to crush Zansul’s ambitions and safely return with the Ultra Particles to save their friend?

Code worships Isshiki Otsutsuki, who was defeated by Boruto and his friends. In order to meet a certain person, he visits the facility that formerly belonged to Boro. Like Kawaki, Code miraculously survived the experiments intended to help select a vessel for Isshiki—and he possesses greater power than even Jigen. He has vowed revenge against Boruto and Kawaki for destroying Isshiki.

Meanwhile, Claw Marks left by Code are discovered just outside of the Hidden Leaf Village. While the Hokage and the others take precautions, Boruto proposes an idea to Kawaki.

In order to gain the strength to fight Code, Boruto invites Kawaki to train, along with Sarada and Mitsuki. Unfortunately, because Kawaki is in a rush, they end up arguing about their training methods.

Meanwhile, at Boro’s facility, Eida has awakened. Eida is another one of Amado’s creations who has the power of the Senrigan, which allows her to see events in the present and the past. Code is powerless against her other ability…

With the disappearance of his Karma, Kawaki has lost his powers. He becomes worried that he won’t be able to protect Naruto or the village he cares for. Seeming to know what Kawaki is thinking, Amado verbally provokes him. Sumire becomes worried that Amado is planning something.

Meanwhile, Code teams up with Eida to get his revenge. Eida introduces him to another person who will be helping them.

Due to the risk that Code might attempt to kill Boruto and Kawaki, guards are assigned to them. Boruto is sick of being watched every day. Meanwhile, Kawaki overhears a conversation between Shikadai and Inojin and learns how to slip past his guard and the Village’s sensory system. Once he decides he must do whatever it takes to protect Naruto and the Hidden Leaf, he jumps into action. Despite their keen sensory abilities, Naruto and the Village’s sensory team are unaware of what’s happening. But Boruto feels a strange sensation that allows him to detect Kawaki’s movements.

Boruto arrives to help Kawaki defeat Code. In order to match Code’s incredible combat abilities, Boruto activates his Karma. In response, Code activates his own Karma. As the battle intensifies, Kawaki becomes worried that Momoshiki might take control of Boruto’s consciousness. Meanwhile, in the Hidden Leaf Village, Boruto and Kawaki had disappeared without anyone noticing. Naruto decides to do his own investigation to find out where they went.

Amid a fierce battle, Kawaki’s fears come true, and Momoshiki takes control of Boruto. Kawaki watches as Boruto overwhelms Code as Momoshiki. Then Naruto arrives with Shikamaru. Kawaki is concerned for Naruto’s safety as one of Code’s targets, but despite his wishes, Naruto takes on Code as the Hokage. Unfortunately, Code takes Shikamaru hostage, and in his desire to settle his grudge, Momoshiki joins him. Naruto faces an extremely dangerous situation.

Boruto makes a desperate decision to prevent Momoshiki from taking over his consciousness again. Meanwhile, Kawaki drives back Code using the Karma that Amado revived. Willing to do whatever it takes to eliminate anyone who is a threat to Naruto, Kawaki fights with overwhelming power. Shikamaru is shocked by his strength, and Code learns the difference in their powers. Boruto and Kawaki have overcome various obstacles as brothers, but a troubling shadow begins to loom over their relationship. As Momoshiki once said, the fateful moment that will take everything from Boruto is approaching!