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.

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!

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!

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?!

Sasuke sends a message to Naruto about a man possessing the Sharingan. Upon receiving the intel, Naruto rushes to meet with Sasuke. Meanwhile, Sarada, who has doubts about who her real mother is, joins Cho-Cho, who is about to set out on a journey to find her “real parents.” Upon learning that Naruto is on his way to meet Sasuke, they go after him. But danger looms when they come under attack.

Sarada arrives at the tower where her father is, only to be hurt by Sasuke's surprising words and actions. Naruto and Cho-Cho can hardly bear to watch the awkward exchange between father and daughter, and try to think of something to help. But the party is attacked by a father-son duo who call themselves "Shin Uchiha," and who possess the Sharingan! Meanwhile, Sakura learns that Sarada has gone to meet her father.

Naruto and Sasuke fight against Momoshiki Otsutsuki. Momoshiki gets defeated, but he's helped by Katasuke and his Scientific Ninja Tool. In the end, Boruto puts an end to Momoshiki's life. While dying, Momoshiki talks to Boruto and gives him the Karma Seal.

Boruto's new mission is to guard Tento, who is obsessed with ninja and collecting X Cards. He begs Boruto to teach him ninja skills, and Boruto thinks this will be a good opportunity to knock some sense into Tento. Meanwhile, the Mujina Gang, which had been laying low after Team 7’s infiltration mission at Hozuki Castle, rears its ugly head.

A training class on Medical Ninjutsu is to be held, and each team must send a representative. Sarada is chosen for Team 7. Despite Sakura being a Medical Ninjutsu specialist, Sarada doesn't have a knack for it and being a participant fills her with anxiety.

Amid a fierce battle, Kawaki’s fears come true, and Momoshiki takes control of Boruto. Kawaki watches as Boruto overwhelms Code as Momoshiki. Then Naruto arrives with Shikamaru. Kawaki is concerned for Naruto’s safety as one of Code’s targets, but despite his wishes, Naruto takes on Code as the Hokage. Unfortunately, Code takes Shikamaru hostage, and in his desire to settle his grudge, Momoshiki joins him. Naruto faces an extremely dangerous situation.