Team 7's original mission evolves into a rescue operation after Kiri is kidnapped. The team must face a formidable genjutsu user as well as a skilled sword user. Following Konohamaru's orders, the team successfully rescues Kiri. But Konohamaru is captured and the trio must battle the enemy alone while protecting Kiri.

The White Snake Sage tells Boruto to bring back the "Reverse Scale" from Garaga, a troublesome snake. Boruto and his friends head deeper into Ryuchi Cave and are confronted by a giant serpent. It is Garaga, the very one they seek, but its sheer power has the gang backed into a corner. Meanwhile, Moegi reports that Mitsuki's disappearance might involve someone who has access to crucial village secrets.

Boruto and the others work together to obtain the Reverse Scale from Garaga. But the battle proves difficult, as Garaga has the power to sense the location of its enemies and turn them into stone. In the midst of battle, the team notices inconsistencies in Garaga's moves and comes up with a successful strategy to subdue him. Boruto is seized with a strange feeling and makes Garaga a proposition.

Jugo is suffering from the effects of the drug that activates the power of the cursed seals. Somehow or another. Boruto and Suigetsu want to try to save him, but they are rendered unable to move because of being injected with a tranquillizer. Meanwhile, it’s time for the migratory birds to set off.

Boruto's quick thinking exposes Urashiki's trick that enables him to see into the future and they manage to inflict some damage. But before they can breathe a sigh of relief, Urashiki emerges again with an even stronger move, and they're back in the same predicament!

Enko Onikuma—one of Boruto's former classmates and a member of Team 40— was possessed by a Summoning Beast as a child. Now, she can manifest its enormous power. But lately, she hasn't been able to control her power, hindering her work on missions. Meanwhile, Ibiki Morino approaches Enko and tells her that she'll be working under him going forward.

Boruto and the others can't help but feel that Kokuri is hiding something from them. Meanwhile, Tsukiyo, a lieutenant in the Mujina Gang who's also imprisoned in Hozuki Castle, schemes to get Kokuri transferred to Hozuki Castle II, where his henchmen lie in wait.

Separated from Boruto and Sarada, Konohamaru battles Victor. But someone unexpected shows up to fight alongside him. Meanwhile, Boruto and Sarada are trying to defeat Deepa to even the score, but he still proves to be a formidable opponent despite all of their training.

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.

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.

The reformed Team 7 launches a series of attacks on Boro. But even when they land successful attacks, Boro instantly revives himself with his extraordinary regeneration powers.

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.

Kawaki enrolls at the Ninja Academy and begins classes as a freshman with Himawari and the others. But it’s actually a secret mission to protect a princess from assassins. This is kept a secret because she’s come from abroad to study. Since it is a personal request from Naruto, Kawaki decides to attend the academy hesitantly, where the students are younger than him. Kawaki’s difficult school life with an unreliable teacher named Hana Kaka and his unique young classmates begins!

Kawaki and Himawari participate in a training session in the forest near the academy. The class is split into three-person teams and Kawaki ends up on a different team from Kae. Anxious about losing sight of Kae, Kawaki is unable to focus and ends up burdening his assigned team. Kae is lured away by a mysterious person and disappears. Fearing that she is in danger, Kawaki and Himawari rush to find her.

The Academy students are at the hospital to visit Hana, who struggles to remember the day of the attack. At the Hokage's palace, Kawaki is relieved of his mission for not reporting the presence of the assassin in time.

The assassin targeting Kae has finally been revealed. Because of their previous clashes, Kawaki knows they are a powerful foe. He decides to chase after the assassin by himself to prevent putting any more students in danger. But Kawaki finds it difficult to do that without knowing where the assassin is; what’s more, his classmates desire to work together to chase down the assassin and save Kae. And so, the entire class begins their pursuit!

Boruto dozes off on Thunder Train and wakes up in an unfamiliar location along with the other passengers. A mysterious individual known as Ouga forces them to participate in a game of death disguised as an experiment—who will successfully beat this game and make it out alive?!

Boruto reawakens to find he’s back where he first found himself.

Seeking information related to the Ultra Particles, Sasuke searches the cellar of the room belonging to Zansul, the director of the Observatory, while a messenger of the prime minister is visiting from the capital. To buy some time, Sakura transforms into the messenger. While Zansul is distracted, Sasuke tries to sneak into the basement, but they start to get anxious when things don’t go according to plan. Meanwhile, Zansul tells Sakura something disturbing.

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.