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!

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.

The shadowy, warped chakra that only Boruto can see takes over more people, causing them to rampage. It only affected people within the Academy at first, but now it’s extending its reach into the village. Can it be stopped? And later, a Visual Jutsu places Boruto within a dream—and afterward, Boruto declares the dream has awakened his Byakugan, the Kekkei Genkai unique to his mother’s Hyuga Clan. Naruto does not believe him, so Boruto seeks advice from his grandfather, Hiashi Hyuga.

Boruto nicknames the mysterious shadow “The Ghost” and is excited when he and his friends Shikadai and Mitsuki decide to solve the recent “Ghost Incidents.” Shino secretly lends Boruto a helping hand by giving their class an assignment to research different workplaces. Meanwhile, Sai, who once served in The Foundation of the ANBU Black Ops, makes a big discovery while investigating the same incident under orders from the Hokate.

The late Danzo Shimura was the founder and leader of the Foundation, an elite branch of the ANBU Black Ops. The recent incidents have been masterminded by someone who had sworn to carry on Danzo's wishes. Boruto is able to enter another world with his strange "eye." The perpetrator wields the Gozu Tennou, a weapon that relies on the power of the beast Nue, and is set on destroying the village. Boruto desperately tries to dissuade them, but can Boruto's thoughts unleash a curse from the past?!

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.

Boruto and his classmates decide to go camping to try to catch the mysterious fish, the Eternal Carp, said to be unforgettably delicious. With graduation coming up this could be the last time the class does something together, so Boruto figures this is the perfect opportunity to catch one, but the fish proves to be very elusive.

Boruto and his classmates take their first step as genin and start forming their basic shinobi three-man squads. The members are matched according to their ability and compatibility. Boruto was counting on teaming up with Shikadai, but is disappointed when he opts to be part of the "Ino-Shika-Cho" trio, like his dad. Boruto finds himself teamed up with Sarada and Mitsuki. Since he and Sarada have issues with this matchup, they file a direct appeal to the Hokage to overturn this decision.

Team 7 enters the mine where the thieves had been hiding out, only to be attacked by a powerful, strange-looking White Zetsu. They find out the mine connects to a ruin belonging to Kaguya Otsutsuki. Team 7 decides to investigate and engage the White Zetsu. As they proceed deeper and deeper into the mine, they make a shocking discovery!