The Hidden Leaf Village is located within the Land of Fire, one of the Five Great Shinobi Nations. Boruto Uzumaki lives here and he's the son of the village leader, Naruto Uzumaki, the Seventh Hokage. One day, Boruto saves a boy named Denki Kaminarimon, who's being picked on. Denki is physically weak, so he is unable to stand up to the bullies. On his way to the entrance ceremony at the Ninja Academy, Boruto sees Denki again. He notices that his chakra is warped and that he is acting strangely.

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...

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?

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…

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.

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 White Snake Sage tells Boruto to bring back the "Reverse Scale" from Garaga, a troublesome snake. Boruto and his friends head deeper into Ryuchi Cave and are confronted by a giant serpent. It is Garaga, the very one they seek, but its sheer power has the gang backed into a corner. Meanwhile, Moegi reports that Mitsuki's disappearance might involve someone who has access to crucial village secrets.

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.

Boruto, Sarada, Mitsuki, and Kawaki arrive at the dimension that Naruto is trapped in, but Boro is there waiting for them. The four create a team with Sarada leading them to fight Boro, who uses a black mist to paralyze his enemies.

Traveling merchants have been attacked by vicious robbers. Wasabi, Namida, and Tsubaki of Team 15 are sent to the site of the incident to investigate. Tsubaki finds a clue that seems to point to samurai from her homeland, the Land of Iron. Furthermore, the clue belongs to a certain person that makes Tsubaki tremble in fear. That person is someone that she respected long ago, a fellow apprentice with whom she trained and honed her swordsmanship with—someone with whom Tsubaki shares a certain fate!

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

Boruto makes a desperate decision to prevent Momoshiki from taking over his consciousness again. Meanwhile, Kawaki drives back Code using the Karma that Amado revived. Willing to do whatever it takes to eliminate anyone who is a threat to Naruto, Kawaki fights with overwhelming power. Shikamaru is shocked by his strength, and Code learns the difference in their powers. Boruto and Kawaki have overcome various obstacles as brothers, but a troubling shadow begins to loom over their relationship. As Momoshiki once said, the fateful moment that will take everything from Boruto is approaching!