After being suspended for the uproar he caused at the entrance ceremony, Boruto makes his way to the academy for the first time. His classmates ostracize him for being the son of the Seventh Hokage and for being suspended. Iwabe Yuino, one of Boruto's classmates, picks a fight with him. Iwabe is an older student who has a keen sense for battle, but was held back a year for his bad behavior. At first, Boruto ignores him no matter what he says. But when he sees Iwabe punch Denki for telling him to stop, Boruto can't ignore him any longer.

A new student named Mitsuki from the Hidden Sound joins Boruto's class. A student named Mitsuki has transferred into Boruto's class from Hidden Sound Village. He overwhelms Iwabe in sparring and shows his genius by solving difficult problems. However, Boruto and the others are unable to tell what he is thinking. Meanwhile, someone who has been doing repair work on the school, suddenly goes berserk. Boruto and the others rush over. Another side of Mitsuki emerges as he starts muttering strange words.

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.

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.

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 Hidden Leaf Village is filled with excitement upon the arrival of the Kage for the Five Kage Summit. Boruto knows that security is tighter than usual, but he still plans on pulling a big prank. Meanwhile, Sarada has found a new goal, to become the Hokage, and trains hard. Behind closed doors, the Five Kage discuss highly classified intel that Sasuke has obtained involving Kaguya Otsutsuki.

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.

Kawaki goes into town with Naruto to get a new vase to replace the one that he broke. On the way to the Yamanaka Flower Shop, they are joined by Sarada. Unaccustomed to peaceful everyday life, he snaps at Sarada’s attempts to talk to him, and almost attacks a child for bumping into him.

Boruto, Kawaki and the others sense something has happened to Naruto. But before anyone can act, Shikamaru and his subordinates arrive and erect a barrier around the Uzumaki home to contain Kawaki, believing he can't be trusted.

Isshiki regains his true form and goes to the Leaf Village to recapture Kawaki. The Leaf shinobi prepare for his arrival. Boruto is willing to fight, but he becomes frightened at the possibility of losing control of his Karma again.