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!

A new student named Mitsuki from the Hidden Sound joins Boruto's class. A student named Mitsuki has transferred into Boruto's class from Hidden Sound Village. He overwhelms Iwabe in sparring and shows his genius by solving difficult problems. However, Boruto and the others are unable to tell what he is thinking. Meanwhile, someone who has been doing repair work on the school, suddenly goes berserk. Boruto and the others rush over. Another side of Mitsuki emerges as he starts muttering strange words.

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 Ghost incidents suddenly come to an end and Boruto and his classmates are puzzled, but Mitsuki seems to know something they don't. Mitsuki himself realizes he's been undergoing some puzzling changes and questions his classmates in order to figure out his predicament. Soon after, a mysterious chakra begins to spread throughout the village.

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?!

Boruto pulls a prank and is pursued around the village by Naruto. Seeing this, Sarada can't help but be exasperated, but a part of her grows wistful as she thinks of her father, Sasuke, whom she hasn't seen since she was a baby. She begins to feel doubt after she sees a photo of Sasuke with a young woman wearing glasses. Sarada becomes determined to learn the truth. Will the secret of Sarada Uchiha's birth be revealed?!

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.

Tsurushi Hachiya, Kagura's former classmate at the Academy, finds Boruto and his friends from the Leaf irritating, so he kidnaps Denki. Kagura and Boruto set out to rescue him, and they find themselves in a battle against Hachiya and his crew. During the fight, the truth that Kagura has been hiding is revealed!

The field trip comes to an end, and Boruto and his friends prepare to return to Hidden Leaf. Chojuro, the Mizukage, sees them off, but Kagura is nowhere to be seen. The class makes it back to the Leaf Village safely and Boruto is relieved to be home. But Himawari isn't her usual cheerful self. She's been looking forward to the souvenir that Boruto promised her, which he completely forgot to get! Boruto decides to tell the truth and beg for Himawari's forgiveness, but he misses his chance, and things gets worse!

Prior to the graduation exams, it's decided that the students will take part in a three-person interview to discuss their future plans. Boruto, who has passed his ninjutsu courses with flying colors, realizes his path toward becoming a "ninja" has been trouble-free and easy. As the students prepare for their finals, Boruto meets a journalist named Sukea who is doing a story on them. Something about Boruto's indifferent attitude about his future as a ninja raises a red flag in Sukea, and he gives Boruto a warning.

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.

The Byakuya Gang's activities become more brazen in the Hidden Leaf. While some people view them as heroic, noble thieves, Boruto can't get himself to approve of their actions. The genin are told to work together to capture the gang, and security in the village is increased. During this time, Shikadai meets a youth named Ryugi. Despite their age difference, a bond grows between them.

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

The third round of the exams begins, consisting of individual battles held tournament style. Boruto’s first match is against Yurui of the Hidden Cloud, and Shikadai is matched up against Yodo of the Hidden Sand. Sarada and Mitsuki are up against Tarui and Toroi of the Hidden Cloud, while Inojin and Cho-Cho pull Araya and Shinki of the Hidden Sand, respectively. After honing their skills in jutsu and strategy, the intense battles between the young shinobi begin!

Boruto has made his rounds apologizing to everyone for his transgressions during the exam, but Momoshiki's prophecy continues to bother him.

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!

Boruto and friends head for Ryuchi Cave in order to see the White Snake Sage. But it's not a simple task, since they have no clue where it is. They search for miles, becoming hungry and tired. They are near their limit when Ryuchi Cave suddenly appears before them along with mysterious women to guide them. They are told they must pass a series of tests in order to meet the White Snake Sage!

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.

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?