At the suggestion of Shino Aburame, their homeroom teacher, Boruto and his classmates split off into gendered teams to capture flags placed on the roof. Boruto and the rest of the boys' team quickly head for the roof, but they struggle with traps and the girls' team, led by Sarada Uchiha and Chocho Akimichi. Desperate to capture a flag before the girls' team, Boruto tries out a Summoning Jutsu, but he ends up summoning something unexpected!

During a tour of workplaces for their school assignment, Sumire, Wasabi Izuno and Namida Suzumeno get wrapped up in the Ghost Incident and are hurt. Boruto feels bad that he wasn't there to prevent their harm, and becomes more determined to solve the case. With the help of Tayori Kuroyagi the postal worker, along with Shikadai and Mitsuki, the team scans the village more closely. Then Shikadai and Mitsuki realize one possibility from something Boruto says casually.

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?!

Sarada is in shock after Sakura is captured by Shin's jutsu. Even Naruto, with his exceptional tracking skills, is unable to locate her. Then Sasuke discovers countless Sharingan embedded in Shin's arm. Following clues gleaned from Shin's arm, they come upon the laboratory of the heinous Hidden Leaf criminal, Orochimaru, who has been conducting research on Forbidden Jutsu. There, Sarada meets her father's former partners Suigetsu Hozuki and Jugo. She then asks Suigetsu to look into who her real mother is.

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.

Udon Ise the jonin captain of Team 5, issues a direct order from the Hokage to Iwabe, Denki and Metal, which states: "In order to attract more students to the Ninjutsu Department of the Academy, you will appear in a PR video documentary." During the Byakuya Gang incident, the three were under suspension, and could only watch as their genin classmates leapt into action. The trio decide to do their best in the documentary in order to prove their prowess, but Udon seems skeptical...

Round two of the Chunin Exams begins. For the second test, three-man teams must try to capture their rival team’s flags. Sarada and Mitsuki set out for enemy territory while Boruto stays behind to guard their flag. The Senka Triplets from the Hidden Mist attack, and Boruto finds himself in trouble. Boruto considers using the Scientific Ninja Tool that Katasuke gave him, but it's prohibited to do so during the exam

Popular actors Tomaru and Ashina receive death threats from an unknown person, so Team 10 is assigned to a joint mission with Team 7 to guard them. The two teams assemble to get the details of their mission, but Boruto sees a beautiful girl he doesn't remember seeing before…

Orochimaru tells Boruto and Sakura about the White Snake Sage who lives in Ryuchi Cave. On their way there, the two are confronted by Team 10, which is determined to take the two back to the village so that they are not labeled as "rogue" ninja. But there's no way Boruto or Sarada will oblige until they find out the truth from Mitsuki, so they are forced into confrontation using everything they've got!

The team finds Ohnoki, but he flatly refuses to help. On top of which, they are attacked and separated. This leaves it up to each member to make it to the rendezvous point on their own. Meanwhile, Mitsuki is being shown around Kokuyou’s hideout.

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.

The cause is still unknown, but they are successively discovering birds that are under control of the power of the cursed seal. Boruto and his comrades from Team 7 are with Tosaka: They are running around together with Juugo, who can absorb the power of cursed seals. Boruto and his comrades continue to rescue the birds by using tranquilizers, so that Juugo and them won’t be controlled by the cursed seal again. However, an incident occurs where they lose all of their tranquilizers.

Mirai, Kakashi, and Guy travel with Tatsumi to a village with a secret hot spring, but they find the hot spring covered by a boulder! Luckily, Choji drops in, armed with the Akimichi Clan’s Secret Super Expansion Jutsu, but he’s too hungry and can’t utilize the full extent of his abilities!

A coded message believed to have been left by Funamushi reveals that the Hidden Mist Village is in danger. Kagura tells Boruto and the others of his plan to stop the enemy at a village on the route there. Everyone hurries to the destination, and it turns out Kagura lived in this village when he was little and has many fond memories of it. When Boruto and the others arrive, they try to get people to help them as they rush to prepare their plan to protect the village and the Hidden Mist!

Sarada, Mitsuki, and Boruto decide to meet with the Mizukage. Chojuro is heading into battle against the pirates, so Boruto and his friends ask the shipbuilder Kajiki for help. Thanks to Kajiki, they manage to reach Chojuro, but when they try to reason with him to stop the battle… Meanwhile, Ikada sails the raging seas with the intent to destroy the Shinonome 1, the brand-new power plant developed by the Land of Water.

Boruto, Sarada, and Mitsuki hold a special lecture at the Academy for freshmen like Kawaki and Himawari. The teacher in charge, Hana, will also speak, but unlike Boruto and his team—who have actual mission experience and flashy jutsu like the Rasengan that appeal to the students—she can only use conservative jutsu, so she feels inadequate as a teacher and becomes depressed. A mock training activity prepared by the trio causes the class to become deeply divided, and Hana struggles to bring the class together again.