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.

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?!

Determined to rescue Sakura, Sarada pursues Shin with Sasuke, Naruto, and Cho-Cho. After brutal battles with Shin's clones along the way, Sarada is surprised to see the bond of trust between Sasuke and Sakura, who haven’t seen each other in years. But suddenly, Shin orders his children to kill the intruders. Since her parents share a bond of trust and love, will Sarada's journey to learn the secret of her birth reach a conclusion?

Chojuro leads Boruto and Sarada to the location where Shizuma and his "New Seven Shinobi Swordsmen" are based. Shizuma uses his jutsu to create a fog that clouds the trio's vision, and they end up getting separated. Sarada is forced into one-on-one combat with a kunoichi, Buntan Kurosuki, who wields the Lightning Blade, Kiba the Fang! In the thick fog, Sarada uses her Sharingan, but her enemy is stronger than expected. Driven into a corner, she comes up with a counterattack. Meanwhile, Boruto goes up against none other than Kagura.

It is time for the graduation exams. Boruto and the others complete the first-round written exam and move on to the next. The second round has the students facing off against Kakashi—the previous Sixth Hokage—and the academy instructors in actual combat situations. With the goal to "steal the bell" from Kakashi, every student rushes into action. However, the going is rough against Kakashi and the teachers who guard him. Somehow, Boruto reaches Kakashi first, but the Sixth Hokage shows no mercy. After a tough fight, he coldly tells Boruto that he's not suited to become a ninja!

Team 7 sets out on their first mission. Their client is a village who has been plagued by bandits, and their mission is to eradicate them. They meet Kiri, a young girl who has just been installed as the village head after her father's sudden death. The team soon realizes that this mission is far more dangerous and complicated than first expected.

Naruto and Sasuke are greatly overwhelmed by Isshiki's abilities. As a last resort, Kurama offers Naruto a chakra mode called Baryon Mode, which grants him immense power. The intensity of this power, however, could end his life.

Naruto and the others are exhausted from their battle with Isshiki. Suddenly, Boruto attacks Sasuke. Momoshiki has taken control of Boruto’s consciousness and stands before them as an enemy. Kawaki desperately calls out to Boruto to snap him out of it. Unfortunately, his words are unable to reach him. Sasuke tells Kawaki a way to bring back Boruto’s consciousness. In order to save Boruto, Kawaki attempts a risky plan using a jutsu he only recently learned. While Kawaki and Sasuke fight a desperate battle, Naruto finally runs out of strength. As his consciousness fades, he and Kurama quietly reminisce about their past.

With Denki as captain, Team 5 is assigned to a mission to transport automated puppets for mining purposes to an island in the Land of Water, to test and operate them, to gather data, and to analyze the results. However, lacking physical strength, Denki isn't very useful and ends up being ridiculed. Will Denki be able to restore his reputation as a ninja and successfully complete his first mission as captain?