Boruto, Shikadai and Mitsuki arrive at the location they are told to go to by Shino. They notice their teacher is acting different than he usually does— and Shino suddenly attacks them! Shino belongs to the Aburame clan, a clan of Insect Users. He unleashes a swarm of Parasitic Insects. Boruto and the others can't match the skill of someone who's a jonin. But even in this situation, Mitsuki remains calm and coldly stares at Shino.

Under his father and grandfather’s guidance, Boruto spars with his aunt Hanabi. Boruto has sought this match in order to win acceptance from his father, but no matter how hard he tries, he can’t activate his Byakugan in any form. He begins to doubt that he even saw the shadowy warped chakra at all, and feels even worse when people begin to think he lied. But then Boruto sees another person being manipulated by the mysterious shadow.

After Mitsuki reveals more information about the Ghost incidents, Boruto is determined to find and stop the culprit! Meanwhile, Seventh Hokage Naruto and his top advisors are shocked to learn who the perpetrator is from the results of Sai's investigation. Just then, Nue—an enormous otherworldly beast—appears! The imminent danger to the village forces the Sixth Hokage, Kakashi, out of retirement!

Exam day is fast approaching, and everyone at the Academy begins preparing for them. Repeating a grade is a possibility if you fail a test. Denki, who lacks skills in ninjutsu, is having a hard time using chakra to climb walls. And as usual, Iwabe can't wrap his head around what he's studying. Boruto and the others try to help them train and study, but end up making things more confusing for the two. Will Denki and Iwabe avoid being held back?

The Uzumaki household is thrown into chaos when Himawari, Boruto's younger sister, catches a cold. Naruto rarely comes home since he became Hokage, and Boruto's anger toward him grows especially because his sister is so sick.

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'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.

Team 7 sets out on their first mission. Their client is a village who has been plagued by bandits, and their mission is to eradicate them. They meet Kiri, a young girl who has just been installed as the village head after her father's sudden death. The team soon realizes that this mission is far more dangerous and complicated than first expected.

The third round of the exams begins, consisting of individual battles held tournament style. Boruto’s first match is against Yurui of the Hidden Cloud, and Shikadai is matched up against Yodo of the Hidden Sand. Sarada and Mitsuki are up against Tarui and Toroi of the Hidden Cloud, while Inojin and Cho-Cho pull Araya and Shinki of the Hidden Sand, respectively. After honing their skills in jutsu and strategy, the intense battles between the young shinobi begin!

The match between Cho-Cho and Shinki of the Hidden Sand begins. Confronted by a foe who is unbelievably calm and menacing, Cho-Cho assumes a seriousness that she rarely reveals as her teammates watch and cheer her on. Boruto and Shikadai's match is next, and the moment nears when the two friends will face off against each other for the first time!

Momoshiki, Kinshiki and Urashiki of the Otsutsuki Clan suddenly appear in the arena filled with spectators. Using his Scientific Ninja Tool, Boruto hurls jutsu after jutsu to no avail against Momoshiki, who is targeting Naruto. Meanwhile, Urashiki is curious about Mitsuki's strange power and goes after him, but he is confronted by Gaara along with the Mizukage Chojuro. Naruto and the other ninja do all they can to protect the citizens, and for the first time, Boruto witnesses the magnitude of his father's power in real combat.

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

The first Five Kage Summit since the attack by the Otsutsuki Clan is held in Hidden Leaf. The current Kage as well as their predecessors assemble, except the Third Tsuchikage, Ohnoki. Boruto and Team 7 have been assigned security duty, but Boruto gets bored and lets his guard down. Then by chance, they encounter Ohnoki.

Orochimaru tells Boruto and Sakura about the White Snake Sage who lives in Ryuchi Cave. On their way there, the two are confronted by Team 10, which is determined to take the two back to the village so that they are not labeled as "rogue" ninja. But there's no way Boruto or Sarada will oblige until they find out the truth from Mitsuki, so they are forced into confrontation using everything they've got!

The White Snake Sage tells Boruto to bring back the "Reverse Scale" from Garaga, a troublesome snake. Boruto and his friends head deeper into Ryuchi Cave and are confronted by a giant serpent. It is Garaga, the very one they seek, but its sheer power has the gang backed into a corner. Meanwhile, Moegi reports that Mitsuki's disappearance might involve someone who has access to crucial village secrets.

Mitsuki heads toward Kokuyou and Sekiei's homeland, the Land of Earth. Meanwhile, thanks to the power of the White Snake Sage, Boruto and the others learn that Mitsuki is with Hidden Stone Ninja, and they also head for the Land of Earth. Each side has their own agenda, but will they be able to meet up successfully?

Mitsuki visits Orochimaru’s research facility because he’s not feeling well. Mitsuki explains to Orochimaru and Log that he never used to dream during sleep, but has recently begun to have them. Hearing Mitsuki’s story, Orochimaru thinks of a solution.

Moved by Tatsumi’s efforts to accomplish her goal all by herself, Mirai decides to help her even though she's still in the middle of her mission.

Extreme Ninja Cards, featuring famous shinobi from history, is the most popular game in recent times. As Boruto and his friends eagerly collect the cards, they realize they are still missing their former teacher, Shino Aburame, and Metal’s father, Rock Lee! They also learn that there’s only one space left in the upcoming series! A fierce battle begins between Boruto, who thinks it should be Shino, and Metal, who stands behind his father. Which candidate will make the final slot?

Boruto and Konohamaru pay a visit to Remon's village, but are puzzled by Remon's cold demeanor. It turns out that Remon is a descendant of the Souma, a family that has protected the village from goblins for many generations. Thus, she is not allowed to leave the village freely. Furthermore, an important ritual is to be held shortly, so Kankitsu Akitsuki, Remon's childhood friend, imprisons her to prevent her from seeing anyone.

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 becomes fascinated by Jiraiya, Naruto's former mentor. Inspired to train, he goes to Sasuke's house, where Sarada mentions Jiraiya's novel. Convinced that reading the novel is the fastest way to learn about Jiraiya, the search for Make-Out Tactics begins!

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.

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.

Ikada returns home after learning that his sister has been severely injured in battle. He spends the next few days looking after her and is visited by Funamushi’s son Kobuna. Kobuna asks Ikada if he will join the fight. Ikada tells him that he is not suited for battle. Despite his feelings, his father Araumi and the other members of the Funato Clan are annoyed that he isn’t joining the fight.