The Yamanaka Clan, who have been tracking the village’s ingoing and outgoing traffic with their advanced sensory abilities, spearheads a plan to create a new sensory system and an operational test is conducted.

A memorial service is being held in remembrance of the many fallen from the Fourth Great Ninja War. Shikamaru and Ino reminisce about their fathers who died carrying out their duties until the very end in the hopes of a better future. Meanwhile, Ao, an aide to the Fifth Mizukage Mei, pays a visit to the Village Hidden in Leaves.

The mysterious organization known as the Kara is about to take one of their plans to the next stage that involves a crucial item called a “Vessel.” However, having his own ambitions, Victor secretly panics as he tries to keep his true objectives hidden from Jigen, leader of the Kara, and the other core members

Boruto, Sarada and Mitsuki are assigned to carry out Team 7’s missions by themselves until Konohamaru returns from an unexpected assignment. Boruto runs into Mugino in town and ends up going to his home at Mugino’s invitation.

Son of Naruto Uzumaki, Boruto, follows his father's footsteps along with his friends to become great ninja. Throughout all their adventures, Boruto is determined to make his mark in the ninja world and live outside of his father's shadow.

After the Chunin Exams, Katasuke has returned to work at the invitation of the Hokage. Upon seeing him, Boruto becomes annoyed thinking about what happened during the exam. Team 7 is given a mission to escort Katasuke and transport a Scientific Ninja Tool. Stuck on a mission he doesn’t like, Boruto runs into Ao while aboard the Thunder Train headed to their destination.

Team 7 has arrived at a high-tech research center along with Katasuke. There, they end up running into some familiar faces. The mission has ended without incident, and Boruto is ready to head home. However, there’s more they must do. Boruto and his friends end up cooperating in a test-run of a Scientific Ninja Tool that is under development. Boruto is unhappy at first, but as the test run continues his feelings start to change. As that happens, Team 7 is given a new urgent assignment from the Hokage.

After finding out that Konohamaru and Mugino have gone missing, Team 7 is ordered to go to their last known location and investigate what happened. Team 7 and Katasuke arrive at the airship wreckage, but are attacked by strange puppets.

Team 7 learns that Ao is now an enemy that works for Kara. After Mugino's plan allows them to escape, they begin to strategize on how to handle the situation. Meanwhile, the members of Kara learn that there may be a traitor among them.

The showdown between Team 7 and Ao begins. Team 7 works together to bring Ao down with various attacks and jutsu, but he proves to be a difficult adversary due to his use of scientific ninja tools.

After Ao's defeat, Koji Kashin appears before Team 7 and attempts to ensnare them in a sealing jutsu and eliminate them. Konohamaru breaks free and takes him on, but during the battle, the mark on Boruto's hand activates.

Koji Kashin retreats from battle after seeing that Boruto has a "Karma" mark on his hand. Shortly after, Team 7 discovers a battle site where a boy lies unconscious. Much to everyone's shock, the boy possesses the same mark as Boruto.

Boruto and the others learn that the boy named Kawaki is the target that Kara has been seeking. They watch on as a battle rages between Kawaki and the Kara Outer, Garo, and are shocked by the young man's capabilities.