Prior to entering the Ninja Academy, Boruto meets a boy named Denki, who is being forced to join the academy for the sake of his father's company.

After being suspended for the uproar he caused at the entrance ceremony, Boruto makes his way to the academy for the first time. His classmates ostracize him for being the son of the Seventh Hokage and for being suspended. Iwabe Yuino, one of Boruto's classmates, picks a fight with him. Iwabe is an older student who has a keen sense for battle, but was held back a year for his bad behavior. At first, Boruto ignores him no matter what he says. But when he sees Iwabe punch Denki for telling him to stop, Boruto can't ignore him any longer.

Boruto's classmate, Metal Lee, is very dilligent and is skilled at taijutsu. Unfortunately, he gets nervous easily and is unable to do his best when people are watching him. One day one of his classmates, Shikadai Nara, says something that enrages Metal, who attacks Shikadai the next day. Caught in the middle, Boruto notices that Metal's chakra is warped, just like Denki's.

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 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.

Boruto, Shikadai and Mitsuki arrive at the location they are told to go to by Shino. They notice their teacher is acting different than he usually does— and Shino suddenly attacks them! Shino belongs to the Aburame clan, a clan of Insect Users. He unleashes a swarm of Parasitic Insects. Boruto and the others can't match the skill of someone who's a jonin. But even in this situation, Mitsuki remains calm and coldly stares at Shino.

Cho-Cho's scared because she thinks she's being watched by someone, so she decides to catch them in the act. She succeeds in snagging Magire Kakuremino, and it turns out he wasn't watching Cho-Cho, but Sumire, the class rep, whom he secretly likes. Cho-Cho urges him to declare his love, and at first Magire hesitates. But he takes the leap and tells Sumire how he feels!

The shadowy, warped chakra that only Boruto can see takes over more people, causing them to rampage. It only affected people within the Academy at first, but now it’s extending its reach into the village. Can it be stopped? And later, a Visual Jutsu places Boruto within a dream—and afterward, Boruto declares the dream has awakened his Byakugan, the Kekkei Genkai unique to his mother’s Hyuga Clan. Naruto does not believe him, so Boruto seeks advice from his grandfather, Hiashi Hyuga.

Under his father and grandfather’s guidance, Boruto spars with his aunt Hanabi. Boruto has sought this match in order to win acceptance from his father, but no matter how hard he tries, he can’t activate his Byakugan in any form. He begins to doubt that he even saw the shadowy warped chakra at all, and feels even worse when people begin to think he lied. But then Boruto sees another person being manipulated by the mysterious shadow

Boruto nicknames the mysterious shadow “The Ghost” and is excited when he and his friends Shikadai and Mitsuki decide to solve the recent “Ghost Incidents.” Shino secretly lends Boruto a helping hand by giving their class an assignment to research different workplaces. Meanwhile, Sai, who once served in The Foundation of the ANBU Black Ops, makes a big discovery while investigating the same incident under orders from the Hokate.

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.

After Mitsuki reveals more information about the Ghost incidents, Boruto is determined to find and stop the culprit! Meanwhile, Seventh Hokage Naruto and his top advisors are shocked to learn who the perpetrator is from the results of Sai's investigation. Just then, Nue—an enormous otherworldly beast—appears! The imminent danger to the village forces the Sixth Hokage, Kakashi, out of retirement!

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?!

The ghost incident that threatened the Hidden Leaf Village is over, and now Boruto is unable to awaken the mysterious power he used. Things return to normal in the village and the Academy, but one thing still troubles Boruto and his classmates...

[Filler] Exam day is fast approaching, and everyone at the Academy begins preparing for them. Repeating a grade is a possibility if you fail a test. Denki, who lacks skills in ninjutsu, is having a hard time using chakra to climb walls. And as usual, Iwabe can't wrap his head around what he's studying. Boruto and the others try to help them train and study, but end up making things more confusing for the two. Will Denki and Iwabe avoid being held back?

[Filler] Sarada agrees to return a teddy bear to a young patient at the hospital, but she forgets it on the train and goes into a panic. Despite having dismissed Boruto and the boys for sitting on the roof of the train, Sarada does exactly that in her desperate search for the toy. Cho-Cho happens to see Sarada and takes her to the station’s lost and found. Sarada retrieves her package and all is well, until…

[Filler] The Uzumaki household is thrown into chaos when Himawari, Boruto's younger sister, catches a cold. Naruto rarely comes home since he became Hokage, and Boruto's anger toward him grows especially because his sister is so sick.

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?!

Sasuke sends a message to Naruto about a man possessing the Sharingan. Upon receiving the intel, Naruto rushes to meet with Sasuke. Meanwhile, Sarada, who has doubts about who her real mother is, joins Cho-Cho, who is about to set out on a journey to find her “real parents.” Upon learning that Naruto is on his way to meet Sasuke, they go after him. But danger looms when they come under attack.

Sarada arrives at the tower where her father is, only to be hurt by Sasuke's surprising words and actions. Naruto and Cho-Cho can hardly bear to watch the awkward exchange between father and daughter, and try to think of something to help. But the party is attacked by a father-son duo who call themselves "Shin Uchiha," and who possess the Sharingan! Meanwhile, Sakura learns that Sarada has gone to meet her father.

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.

Determined to rescue Sakura, Sarada pursues Shin with Sasuke, Naruto, and Cho-Cho. After brutal battles with Shin's clones along the way, Sarada is surprised to see the bond of trust between Sasuke and Sakura, who haven’t seen each other in years. But suddenly, Shin orders his children to kill the intruders. Since her parents share a bond of trust and love, will Sarada's journey to learn the secret of her birth reach a conclusion?

The Hidden Leaf Village is filled with excitement upon the arrival of the Kage for the Five Kage Summit. Boruto knows that security is tighter than usual, but he still plans on pulling a big prank. Meanwhile, Sarada has found a new goal, to become the Hokage, and trains hard. Behind closed doors, the Five Kage discuss highly classified intel that Sasuke has obtained involving Kaguya Otsutsuki.

Boruto and his class head to the Water country, towards Village of the Hidden Mist, for a field trip. Guided by Kagura Karatachi, Boruto and his friends couldn’t believe that a village that is so overflowing with life and modern used to be called the Village of the Bloody Mist, and that children were made to battle each other to the death back then. However, there are ninjas in the Hidden Mist that are unhappy with the current situation of the village too.

Boruto and his friends are being led through the Village of the Hidden Mist by Kagura and the 6th Mizukage, Chojuro, visiting their Academy. The Hidden Mist have increased their attention on sword techniques, and Boruto, seeing this intense view of the lesson, becomes excited. He then requests a bout with Kagura from Chojuro.

Tsurushi Hachiya had been with Kagura throughout the Academy years, and now he finds Boruto a nuisance, and attempts to draw Boruto and his friends out by abducting Denki. In an attempt to save Denki, Boruto and his friends join Kagura, and head towards Hachiya, and battle with a large group of allies that had been gathered against them. During that time, a truth that Kagura had been hiding comes to light.

Kagura makes up his mind to accept the famed sword Hiramekarei from Chojuro, but unwittingly becomes part of a plot set up by Kagura’s old acquaintance, Shizuma Hoshigaki, a man who opposes the new, peaceful shinobi order.

Kagura unlocks the storeroom to let Shizuma take the Mist Blades. The New Seven Ninja Swordsmen begin an insurrection, the end goal being to turn their village back into the Blood Mist Village! News of the rebellion reaches Chojuro and Mei, the current and previous Mizukage. They are determined to execute the perpetrators, along with Kagura, who aided them. In order to change Chojuro's mind, Boruto makes an astonishing announcement.

Chojuro leads Boruto and Sarada to the location where Shizuma and his "New Seven Shinobi Swordsmen" are based. Shizuma uses his jutsu to create a fog that clouds the trio's vision, and they end up getting separated. Sarada is forced into one-on-one combat with a kunoichi, Buntan Kurosuki, who wields the Lightning Blade, Kiba the Fang! In the thick fog, Sarada uses her Sharingan, but her enemy is stronger than expected. Driven into a corner, she comes up with a counterattack. Meanwhile, Boruto goes up against none other than Kagura.

Boruto urges his friend Kagura to return with him, but Kagura rejects him and begins to attack. Although Boruto is desperate to save him, Kagura once again falls under a spell and is unable to defy Shizuma. Then someone steps in between the two as they battle. It's Mitsuki, and he has obtained intel about the rebellion. Just what is the intel, and can Boruto save his friend?

[Filler] 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!

[Filler] Inojin has loved to draw since he was small, and his ninjutsu speciality is the Super Beast Scroll. But one day, he suddenly loses his ability to use his jutsu! Puzzled, he talks to his father, Sai, who uses the same jutsu. Even though Sai is sympathetic, he doesn't give Inojin a way to overcome his slump. Instead he suggests that his son enter into a children's art contest, which Inojin halfheartedly does.

[Filler] 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.

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.

It is time for the graduation exams. Boruto and the others complete the first-round written exam and move on to the next. The second round has the students facing off against Kakashi—the previous Sixth Hokage—and the academy instructors in actual combat situations. With the goal to "steal the bell" from Kakashi, every student rushes into action. However, the going is rough against Kakashi and the teachers who guard him. Somehow, Boruto reaches Kakashi first, but the Sixth Hokage shows no mercy. After a tough fight, he coldly tells Boruto that he's not suited to become a ninja!

Boruto was the first to challenge the graduation exam’s proctor Kakashi, after being the first to arrive at his location, however, he is easily held down. Furthermore, Kakashi criticized not only Boruto himself, but also all his classmates, leading Boruto to become extremely frustrated. Boruto’s classmates arrive, and manage to free Boruto through a combined effort, allowing him to escape from Kakashi. Boruto is uncharacteristically depressed, so his classmates do their best to restore his spirits. Finding himself again, Boruto proposes a strategy to everyone.

Boruto and his friends are successful in becoming apprentice ninja, ‘Genin’, their first step. Firstly, they must form their basic teams to carry out missions in, a three man cell. Boruto expected to group up with his close friend Shikadai; however, Shikadai is forming a cell with Inojin and Chocho, following in their parents’ footsteps of the ‘Inoshikacho’ trio. Boruto then becomes grouped with Sarada and Mitsuki…….

Mitsuki was originally from another village, the Village of the Hidden Sound. But since meeting with Boruto and the others, Mitsuki has decided that he will now remain at the Village of the Hidden Leaf and become a ninja. In the past, Mitsuki has had his memory taken away from him, and had lost his identity, along with what he wants to achieve in life, only to awaken in an unfamiliar laboratory. The mystery that surrounds Mitsuki, and the plethora of thoughts that surround him, has now cleared up for him.

Boruto, Sarada, and Mitsuki have come together and formed ‘Team 7’. The three, led by Jonin Sarutobi Konohamaru, have received their first mission. The mission details the repelling of bandits who have been attacking a village, and making it so that they never come back again. Boruto and the others immediately depart for the village, and come face-to-face with a young woman named Kiri, who is the daughter of the village chief who had suddenly passed away and has inherited her father’s role, and the others who support her.