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.

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.

Boruto's classmate, Metal Lee, is very dilligent and is skilled at taijutsu. Unfortunately, he gets nervous easily and is unable to do his best when people are watching him. One day one of his classmates, Shikadai Nara, says something that enrages Metal, who attacks Shikadai the next day. Caught in the middle, Boruto notices that Metal's chakra is warped, just like Denki's.

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?!

Boruto and his classmates head to the Village Hidden in the Mist in the Land of Water for a field trip. Kagura Karatachi is chosen as the village guide. About the same age as Boruto, Kagura is already an accomplished shinobi and serves as an aide to the Mizukage, Chojuro. Once known as the Blood Mist Village, it's now more modern and bustling than anyone could have imagined. However, dissatisfaction exists among some Hidden Mist Shinobi.

Kagura makes up his mind to accept the famed sword Hiramekarei from Chojuro, but unwittingly becomes part of a plot set up by Kagura’s old acquaintance, Shizuma Hoshigaki, a man who opposes the new, peaceful shinobi order.

The Chunin Exams are fast approaching and everyone’s excited—except for Boruto, which causes everyone grief. During this time, Boruto and his family have a rare chance to be together to celebrate Himawari's birthday, and for once it seems his father has kept his promise...

Unable to contain his anger towards his father for ruining Himawari’s birthday as well as his own, Boruto rushes out to confront Naruto. He runs into Sasuke and unknowingly attacks him but is instantly subdued. Amazed at Sasuke’s strength, Boruto asks him to be his teacher. Sasuke agrees to the request but only after Boruto is able to use the Rasengan. In order to win Sasuke's approval, Boruto trains unusually hard.

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.