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!

Konohamaru tries to rescue Remon by checking up on Kankitsu, but he is caught and forcibly taken back to the Leaf Village. Boruto becomes suspicious when he sees Kankitsu alone and acting as if nothing has happened. He decides to investigate the situation, only to be shocked by the sight that unfolds before him! Meanwhile, Konohamaru is disciplined by the Hokage after receiving a complaint from Remon's village.

While chasing down Urashiki, Boruto and Sasuke get hit with a strange Otsutsuki weapon. They find themselves in the Hidden Leaf, but years before Boruto was born. Although there's no sign of Urashiki, Sasuke thinks they should proceed carefully. Suddenly, a very young Naruto appears with Jiraiya and the two start questioning the "outsiders."

Boruto's grandfather Hiashi's birthday is approaching and there's going to be a small family celebration. Boruto is chosen to select a birthday present, but he doesn't know what will please his grandfather, so he visits the Hyuga household and sneakily gathers information.

Boruto has a dream about the day he defeated Momoshiki Otsutsuki. It ends up bothering him so much that he can't focus on his mission. He then meets Tento, the son of Ikkyu Madoka—the Feudal Lord of the Land of Fire—who’s in the Hidden Leaf for a meeting with the Hokage.

Cho-Cho and Choji go to the sweet shop after their training session, only to be disappointed that they are unusually out of azuki bean sweets. After hearing thieves have been raiding the deliveries, Cho-Cho plans to team up with Anko Mitarashi, her friend in desserts and beloved Ninja Academy instructor, to protect the azuki beans that she loves, and capture the bandits!

Boruto and the others manage to escape Yuuga's barrier, but this time his younger brother Hiruga gets in their way. Like Yuuga, Hiruga will resort to any method to fulfill his mission and uses his jutsu to seal away Boruto and the others. As Boruto tries to break the jutsu, he’s baffled by their rabid fighting style and their willingness to risk their lives.

Konohamaru and his teammates report their findings that the Kara receives outside assistance from people called Outers, and that these Outers may have covertly infiltrated the Five Great Shinobi Nations. Though Naruto feels that, as Hokage, he is responsible for protecting the village, he is unable to decide on a course of action.

Team 7 learns that Ao is now an enemy that works for Kara. After Mugino's plan allows them to escape, they begin to strategize on how to handle the situation. Meanwhile, the members of Kara learn that there may be a traitor among them.

Kawaki goes into town with Naruto to get a new vase to replace the one that he broke. On the way to the Yamanaka Flower Shop, they are joined by Sarada. Unaccustomed to peaceful everyday life, he snaps at Sarada’s attempts to talk to him, and almost attacks a child for bumping into him.

Boruto, Kawaki and the others sense something has happened to Naruto. But before anyone can act, Shikamaru and his subordinates arrive and erect a barrier around the Uzumaki home to contain Kawaki, believing he can't be trusted.

Isshiki regains his true form and goes to the Leaf Village to recapture Kawaki. The Leaf shinobi prepare for his arrival. Boruto is willing to fight, but he becomes frightened at the possibility of losing control of his Karma again.

The final test, this time it's Iwabe vs Wasabi.　The two have a strong competitive spirit and usually clash with each other, but for some reason Iwabae is bewildered by Wasabi's unusual lack of energy. Wasabi, in fact, is feeling overwhelmed by the pressure of representing the hitherto unproven Izuno clan. Iwabeye is angry at Wasabi for setting her own limits on her ability and giving up. ......?　Who will be the victor in this match?

Boruto is visiting the prison when an airship explodes during the ceremony. Just as he is about to rush to the scene, the facility is attacked, so he stays to help Kagura fight off the assailants. Will they be able to stop the attempted prison break of the leader of a gang of pirates?

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.

Kae has been taken away and Kawaki must face a dangerous assassin. Himawari acts as his partner and provides support during the battle. They try to corner the enemy with coordinated attacks, but the enemy proves to be powerful. Meanwhile, their classmates, who had entrusted Kawaki and Himawari to directly confront the assassin, take action in a desire to try to help. Will Kawaki be able to save his precious friends and accomplish his mission?

Ignoring the danger to his own life, Boruto tells the other test subjects to escape while he takes on the person who may be working for Ouga. But they decide to stay and help Boruto fight the suspect.

As they search for Boruto’s whereabouts, Sarada and her team find themselves surrounded by skilled ninja and uncover unexpected information about the incident.