At the suggestion of Shino Aburame, their homeroom teacher, Boruto and his classmates split off into gendered teams to capture flags placed on the roof. Boruto and the rest of the boys' team quickly head for the roof, but they struggle with traps and the girls' team, led by Sarada Uchiha and Chocho Akimichi. Desperate to capture a flag before the girls' team, Boruto tries out a Summoning Jutsu, but he ends up summoning something unexpected!

The Ghost incidents suddenly come to an end and Boruto and his classmates are puzzled, but Mitsuki seems to know something they don't. Mitsuki himself realizes he's been undergoing some puzzling changes and questions his classmates in order to figure out his predicament. Soon after, a mysterious chakra begins to spread throughout the village.

The ghost incident that threatened the Hidden Leaf Village is over, and now Boruto is unable to awaken the mysterious power he used. Things return to normal in the village and the Academy, but one thing still troubles Boruto and his classmates...

Tsurushi Hachiya, Kagura's former classmate at the Academy, finds Boruto and his friends from the Leaf irritating, so he kidnaps Denki. Kagura and Boruto set out to rescue him, and they find themselves in a battle against Hachiya and his crew. During the fight, the truth that Kagura has been hiding is revealed!

Boruto urges his friend Kagura to return with him, but Kagura rejects him and begins to attack. Although Boruto is desperate to save him, Kagura once again falls under a spell and is unable to defy Shizuma. Then someone steps in between the two as they battle. It's Mitsuki, and he has obtained intel about the rebellion. Just what is the intel, and can Boruto save his friend?

It is time for the graduation exams. Boruto and the others complete the first-round written exam and move on to the next. The second round has the students facing off against Kakashi—the previous Sixth Hokage—and the academy instructors in actual combat situations. With the goal to "steal the bell" from Kakashi, every student rushes into action. However, the going is rough against Kakashi and the teachers who guard him. Somehow, Boruto reaches Kakashi first, but the Sixth Hokage shows no mercy. After a tough fight, he coldly tells Boruto that he's not suited to become a ninja!

Boruto's the first to confront Kakashi in the exam. Despite a determined effort, he is immobilized and angered by Kakashi's severe criticism of his class. Shortly after, Boruto's classmates come by to assist and Boruto makes his escape. Although depressed by his own shortcomings, Boruto is able to overcome them and formulate a strategy, thanks to the encouragement of his friends.

The Byakuya Gang's activities become more brazen in the Hidden Leaf. While some people view them as heroic, noble thieves, Boruto can't get himself to approve of their actions. The genin are told to work together to capture the gang, and security in the village is increased. During this time, Shikadai meets a youth named Ryugi. Despite their age difference, a bond grows between them.

The Chunin Exam assembles exceptional genin from each village and pits them against each other in order to assess their abilities. Childhood friends and teammates Konohamaru, Udon and Moegi contemplate whether the genin under their guidance will be able to handle the severity of the Chunin Exam.

The tournament nears its finale, as the matches of Sarada vs. Araya of the Hidden Sand and Mitsuki vs. Shinki of the Hidden San begin! Sarada uses her shuriken and Sharingan skills to attack Araya relentlessly, but he counters her with total ease. Her genjutsu has no effect and she is backed into a corner. In Mitsuki and Shinki's match, the evenly matched duo puts on a show of skills.

Boruto has made his rounds apologizing to everyone for his transgressions during the exam, but Momoshiki's prophecy continues to bother him.

Boruto and friends head for Ryuchi Cave in order to see the White Snake Sage. But it's not a simple task, since they have no clue where it is. They search for miles, becoming hungry and tired. They are near their limit when Ryuchi Cave suddenly appears before them along with mysterious women to guide them. They are told they must pass a series of tests in order to meet the White Snake Sage!

Boruto and Ohnoki head to the rendezvous point, but they stumble into the Hidden Stone Shinobi Training Grounds, which are protected by a barrier. Ohnoki tells Boruto that the only way out of the Training Grounds is to find his heart of stone, something that can only be found once in a lifetime when a person comes to terms with their will.

Sustaining great damage from Mitsuki’s attack, Ku flees the scene. Boruto and Sarada attempt to chase after him, but Kirara blocks their path! Meanwhile, Sekiei watches everything unfold. Shocked and confused by the actions of Mitsuki, Sekiei recklessly attacks him. Not wanting to fight, Mitsuki tries to stop him.

The Nara clan’s chief elder tells Shikadai to quit being a ninja and become a politician in order to increase the reputation of the clan. Shikadai is hesitant, but considers his father’s position and accepts. Boruto and the others are surprised by Shikadai’s sudden decision. Shikadai takes a hiatus from ninja missions and decides to study to become a politician.

A few days into the mission, Mirai visits the hot spring with Tenten, Guy’s former student. But that moment of relaxation is interrupted by Guy yelling about a ghost.

Kakashi goes to the post office—disguised as Sukea, a freelance journalist—to observe Team 25, whose mission is to assist with sorting mail. Houki Taketori, Hako Kuroi, and Renga Kokubou are genin and Boruto's former classmates. As a team, they haven't distinguished themselves, so the missions they are assigned to always consist of simple tasks. Furthermore, they lack teamwork. To find the reason for this, Kakashi decides to talk to Houki, who for some reason dresses just like him.

Boruto and Shinki clash, and they ultimately end up going their separate ways. But an Otsutsuki puppet appears before Shinki. Just then, Boruto arrives with Shikadai and Temari, who were on their way to the Hidden Sand. Even with their help, the Otsutsuki puppet proves formidable. Meanwhile, Urashiki breaks through Gaara’s Sealing Jutsu and begins to move once again.

Boruto and Sasuke end up staying in the Hidden Leaf under the watchful eyes of Naruto and Jiraiya. At first, Boruto feels uncomfortable being with Naruto, but gradually warms up to him. Meanwhile, a group of genin—Sakura, Hinata, and Neji—are summoned for duty along with their chunin leader, Shikamaru. Boruto and Naruto head to the designated meeting place and find something unexpected.

The battle against Urashiki is over, and it's time for Boruto and Sasuke to return to the place where they rightfully belong. Boruto is wistful about leaving Jiraiya and Naruto. Suddenly, Jiraiya makes a request to Sasuke.

It is discovered that a wooden tag used to prevent unauthorized entry into the medical unit has been stolen, and the prison guards begin a search for the culprit. Until the offender is found, all prisoners are locked in their cells. Once the culprit is found, each of their cellmates will be forced into solitary confinement. If this happens and the team becomes separated from Kokuri, their mission could be jeopardized.

Boruto rushes to save Tento, but Shojoji the leader of the Mujina Gang blocks his way. Boruto dodges to protect Tento, but Shojoji and his Corpse Clone Jutsu prove to be too powerful. In the midst of all this, the mark on Boruto's palm reacts and paralyzes him.

Using intel obtained from Shojoji the leader of the Mujina Gang, Sai and Sasuke journey to the Hidden Rain Village to find a location thought to be the hideout of an organization known as "Kara, the Husk.

Boruto and the team finally catch up to the real thieves, two ninja brothers from the Land of Kasumi. Yuga uses a Forbidden Jutsu to summon a monster, and seals it and the team inside a strong barrier. Naruto insists on defeating it and getting out of the barrier. But Mugino argues that unnecessary fighting should be avoided since they don't know how to counter this special jutsu.

Under Kakashi's watchful eye, Boruto succeeds in powering up his own style of Rasengan. And he demonstrates his progress in a battle against an opponent of Kakashi’s choosing. Meanwhile, Sasuke and Sakura switch places to train their daughter. With firm resolve, Boruto and Sarada continue their training and begin to see the results of their hard work.

The Yamanaka Clan, who have been tracking the village’s ingoing and outgoing traffic with their advanced sensory abilities, spearheads a plan to create a new sensory system and an operational test is conducted.

Koji Kashin retreats from battle after seeing that Boruto has a "Karma" mark on his hand. Shortly after, Team 7 discovers a battle site where a boy lies unconscious. Much to everyone's shock, the boy possesses the same mark as Boruto.

In order to get a better handle on their Karmas, Boruto and Kawaki decide to train under more realistic conditions. As Naruto and Himawari watch, they activate their Karmas and confront one another. Meanwhile, Delta joins up with Koji Kashin, who’s still pursuing Kawaki. Somehow, Koji is able to sneak into the village without triggering the Hidden Leaf’s sensory system. Delta is left with no choice but to wait for his return. But when he doesn’t come back, she runs out of patience.

Naruto has been pulled into a different dimension by Jigen. There he encounters Sasuke, who tells him that Jigen is a dangerous person and that they must do whatever it takes to defeat him immediately. Naruto and Sasuke work together to defeat Jigen in a fierce battle, but they struggle against Jigen's advanced fighting abilities and mysterious jutsu. Meanwhile, Boruto gets a bad premonition when his Karma starts acting up, and so he quickly returns home with Mitsuki. Kawaki and Sarada are there, worried about Naruto's safety.

Konohamaru and Sai are given a mission to infiltrate Boro's cult in order to obtain information on Kara and its whereabouts.

The final exam has finally begun. The first match of the individual competition in the form of a real match is the VS Houki.　The twenty-fifth team of Houki and, unusually among their peers, has been involved in the mission of the "Anbu" until now. So, while we don't know what he's up to, Inojin uses his signature technique "Choju Giga" from the very beginning to hunt down Houki. However, as Houki was waiting for a chance, he suddenly lost sight of his opponent's location and the game was reversed. Who will win ......?

In this game, you'll have the chance to take the final exam, but you'll have to be careful not to get caught.

Team 7, with Sarada as captain, are assigned a mission. Mirai, who was on a mission with Konohamaru, returns to the village critically injured. The mission was supposed to be simple, but Mirai reports that the situation has changed drastically. It’s decided that reinforcements will be sent and Team 7 volunteers to go.

The ship carrying Boruto, his friends, and the people of Dotou Island is dead in the water. A shipbuilder Kajiki and his apprentice Ikada happen to pass by and offer to repair the ship at an island of shipbuilders where they live. Upon arriving on the island, Boruto and his friends try to do whatever they can to help while waiting for their ship to be repaired. Meanwhile, in the seas near the Land of Water, a clash between the pirates of the Funato Clan and the Land of Water is becoming unavoidable.

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.

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 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.

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 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.

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.