Boruto and his classmates are invited to tour the Hidden Mist Academy under Kagura and Chojuro's escort. The Hidden Mist emphasizes swordsmanship, and Boruto is awed by their intense training sessions. Chojuro sees Boruto's interest and arranges a sparring match with Kagura, who seems hesitant. Kagura is extremely skilled and has been asked by Chojuro to become the successor to his Great Twin Sword, Hiramekarei, but he has declined.

Boruto and his classmates decide to go camping to try to catch the mysterious fish, the Eternal Carp, said to be unforgettably delicious. With graduation coming up this could be the last time the class does something together, so Boruto figures this is the perfect opportunity to catch one, but the fish proves to be very elusive.

Boruto is dissatisfied with the team's easy and lackluster missions since its first one. Team 7 is assigned to capture a suspect who has barricaded himself inside a bank. Excited to show off his skills again, Boruto and the team rush to the site. But the suspect turns out to be a timid individual who was recently fired. A possibility soon arises that a certain organization could be involved!

Boruto and the other Leaf Genin return to the Hidden Leaf with Mitsuki. However, Mitsuki is detained and subjected to hours of interrogation. And since Boruto and the others have taken actions that would normally banish them from the village, it is decided that they will lose their genin qualification as punishment.

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.

Urashiki appears to steal the chakra of Nine Tails from Naruto, but his attempt is unsuccessful. In order to save Naruto, Boruto, Sasuke and Jiraiya pursue Urashiki. Jiraiya then notices that the malevolent Nine Tails Chakra has started filling the air.

Boruto and his team try to get Kokuri assigned to the same cell, but the warden, Benga, shuts the idea down. Looking for a weakness in Benga, they approach Doragu, the leader among the prisoners, for information they can exploit. Doragu is willing to give them information, but in exchange Boruto and the team must undergo a test of perseverance.

One rainy night, guided by Mikazuki the cat, Mitsuki rescues an injured man. Mysteriously, Mikazuki seems to take a liking to the man who says he’s come to visit his sister who works in the Leaf Village. Soon after, Team 7 is assigned to back up the Leaf Police Force on a security mission. Their client is a president of a company who is being targeted by a serial killer known as "The Rainy Day Killer.

Shikadai, Inojin, and Cho-Cho's Team 10 is assigned to a joint mission with Shinki, Yodo, and Araya from the Hidden Sand. The mission is to find and retrieve an Otsutsuki Puppet that Shikadai had once fought. Team 10 arrives in the Land of Wind and decide to stop at a certain shop. On their way, a man passes them who piques Shikadai's interest. Upon arriving, a chilling scene confronts the trio.

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.

Naruto falls ill, and Sasuke goes to the Tatar Observatory to try to find a cure.