Naruto has been pulled into a different dimension by Jigen. There he encounters Sasuke, who tells him that Jigen is a dangerous person and that they must do whatever it takes to defeat him immediately. Naruto and Sasuke work together to defeat Jigen in a fierce battle, but they struggle against Jigen's advanced fighting abilities and mysterious jutsu. Meanwhile, Boruto gets a bad premonition when his Karma starts acting up, and so he quickly returns home with Mitsuki. Kawaki and Sarada are there, worried about Naruto's safety.

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.

Cho-Cho is injured in an attack by a mysterious ninja and the item that Mozuku had been holding is stolen. Captain Shikadai realizes that this was no ordinary guard mission, but one that makes them the targets of other ninja. He immediately decides to turn back toward home. But Kawaki feels for Mozuku, who was entrusted with the item that would save his people, so he ignores Shikadai's orders and pursues the ninja along with Mozuku. All alone, Kawaki faces a powerful enemy who uses a strange jutsu. Will he be able to protect Mozuku and safely return him to the Land of Calm Seas?

During the battle against Funamushi, Kagura is fatally injured. Boruto becomes enraged and charges at Funamushi, activating his Karma. When the Funato squad retreats, Kagura gives Boruto and the others one final request.

Code worships Isshiki Otsutsuki, who was defeated by Boruto and his friends. In order to meet a certain person, he visits the facility that formerly belonged to Boro. Like Kawaki, Code miraculously survived the experiments intended to help select a vessel for Isshiki—and he possesses greater power than even Jigen. He has vowed revenge against Boruto and Kawaki for destroying Isshiki.

Meanwhile, Claw Marks left by Code are discovered just outside of the Hidden Leaf Village. While the Hokage and the others take precautions, Boruto proposes an idea to Kawaki.