The film opens with a battle between Sasuke Uchiha and an unknown adversary. Many years after the events of the main series, Naruto Uzumaki is the Seventh Hokage of Konohagakure; he is married to Hinata Hyuga, and they have two children, Boruto and Himawari Uzumaki. Boruto is in an elite team under Konohamaru Sarutobi, with Sasuke and Sakura Haruno’s daughter Sarada Uchiha; and a mysterious boy named Mitsuki, as his teammates.
Boruto is upset that Naruto focuses more on his Hokage duties than their family, and thus hates the title of Hokage. Sasuke returns to Konoha to warn Naruto of the powerful enemy he encountered. After Naruto stands up to Himawari’s birthday, Boruto learns about Sasuke from Sarada, he requests Sasuke to train him to become strong enough to surpass Naruto. Sasuke agrees on the condition that Boruto performs the Rasengan which he learns from Konohamaru. When Boruto presents his undersized Rasengan to Sasuke, Sasuke honors his promise despite feeling unconvinced, and teaches Boruto to prepare for the upcoming chunnin exams. Boruto, hoping to finally convince Naruto to spend more time with him, is tempted to cheat in the exam by using a prototype device, Kote, that can store and release jutsu, given to him by the arrogant scientist Katasuke, who wanted his experiment to make for marketing purposes before Naruto shot down the proposal. In the exams, Naruto catches Boruto using Kote to defeat Shikadai Nara, Shikamaru Nara and Temari’s son, in the third stage. He immediately disqualifies his son, and declares Shikadai the winner. Boruto is outraged, but then two figures make their presence known; one of them – Kinshiki Ōtsutsuki.
Alongside his master, Momoshiki Ōtsutsuki, the duo are revealed to be after the Nine-Tails’ chakra inside Naruto to create another chakra fruit like Kaguya Ōtsutsuki had acquired to continue being immortal and invincible. Naruto eventually sacrifices himself to protect everyone, then entrusts Boruto’s safety to Sasuke. The conflict persuades Boruto to see what the Shinobi World really is. Sensing that Naruto is still alive in another dimension, Sasuke allies himself with the other Kages – Gaara, Darui, Chojūro, and Kurotsuchi to rescue him. Boruto insists on joining them to make amends with his father. They arrive in the other dimension to find Naruto bound by the Ōtsutsuki duo, and the four Kage engage Kinshiki in a fight. When the Kage fail to subdue him, Naruto and Sasuke fight as well, but Momoshiki turns Kinshiki into a chakra pill and swallows him to increase his strength. Momoshiki is overpowered, but Katasuke arrives and shoot Momoshiki with a Kote that only restores his strength.
Overpowered by Momoshiki’s strength and left without options, Naruto lends his remaining chakra to Boruto while Sasuke distracts Momoshiki long enough for Boruto to create a giant Rasengan. Boruto blinds Momoshiki’s Rinnegan with his own Vanishing Rasengan. Momoshiki ends up absorbing his own chakra along with Boruto’s giant Rasengan, destroying him. After Boruto reconciles with his father, he resolves to become a ninja who protects the village from the shadows, so he supports Sarada’s dream of being Hokage. It ends with Konohamaru chased by a wild bear; Boruto, Sarada, and Mitsuki jump from the Hokage Monument into midair.
In a post-credits scene, Boruto and Sarada ask Mitsuki who his parents are, and he reveals he is the son of Orochimaru, surprising both of them. Orochimaru himself is seen watching over them.