The Hidden Leaf Village is located within the Land of Fire, one of the Five Great Shinobi Nations. Boruto Uzumaki lives here and he's the son of the village leader, Naruto Uzumaki, the Seventh Hokage. One day, Boruto saves a boy named Denki Kaminarimon, who's being picked on. Denki is physically weak, so he is unable to stand up to the bullies. On his way to the entrance ceremony at the Ninja Academy, Boruto sees Denki again. He notices that his chakra is warped and that he is acting strangely.

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.

Cho-Cho's scared because she thinks she's being watched by someone, so she decides to catch them in the act. She succeeds in snagging Magire Kakuremino, and it turns out he wasn't watching Cho-Cho, but Sumire, the class rep, whom he secretly likes. Cho-Cho urges him to declare his love, and at first Magire hesitates. But he takes the leap and tells Sumire how he feels!

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.

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!

Sarada is in shock after Sakura is captured by Shin's jutsu. Even Naruto, with his exceptional tracking skills, is unable to locate her. Then Sasuke discovers countless Sharingan embedded in Shin's arm. Following clues gleaned from Shin's arm, they come upon the laboratory of the heinous Hidden Leaf criminal, Orochimaru, who has been conducting research on Forbidden Jutsu. There, Sarada meets her father's former partners Suigetsu Hozuki and Jugo. She then asks Suigetsu to look into who her real mother is.

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!