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.

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.

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 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.

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!

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.

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!

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.

Unable to contain his anger towards his father for ruining Himawari’s birthday as well as his own, Boruto rushes out to confront Naruto. He runs into Sasuke and unknowingly attacks him but is instantly subdued. Amazed at Sasuke’s strength, Boruto asks him to be his teacher. Sasuke agrees to the request but only after Boruto is able to use the Rasengan. In order to win Sasuke's approval, Boruto trains unusually hard.

Momoshiki, Kinshiki and Urashiki of the Otsutsuki Clan suddenly appear in the arena filled with spectators. Using his Scientific Ninja Tool, Boruto hurls jutsu after jutsu to no avail against Momoshiki, who is targeting Naruto. Meanwhile, Urashiki is curious about Mitsuki's strange power and goes after him, but he is confronted by Gaara along with the Mizukage Chojuro. Naruto and the other ninja do all they can to protect the citizens, and for the first time, Boruto witnesses the magnitude of his father's power in real combat.

The first Five Kage Summit since the attack by the Otsutsuki Clan is held in Hidden Leaf. The current Kage as well as their predecessors assemble, except the Third Tsuchikage, Ohnoki. Boruto and Team 7 have been assigned security duty, but Boruto gets bored and lets his guard down. Then by chance, they encounter Ohnoki.

Instead of returning home with Boruto, Mitsuki stays with Kokuyou. During this time, Sekiei becomes sick and declines. To recover, Kokuyou returns to his comrades. During his absence, Sekiei asks Mitsuki to teach him what it means to be human. Meanwhile, the Fourth Tsuchikage Kurotsuchi, who had been visiting Ohnoki, her ailing grandfather, is attacked by mysterious assailants.

After Boruto and Sarada part ways with Shikadai and the others, Kirara appears and turns them into “dolls” that must obey her, ordering the two to kill each other. Meanwhile, thinking about Boruto’s words and how his village is becoming something different than what he envisioned, Ohnoki realizes that he’s made a mistake.

Birds are attacking the residents of a village located on the outskirts of the Land of Fire. Boruto's and Sumire’s teams are assigned a joint mission to identify the cause.

Mirai and crew arrive at the hot springs located near the border of the Land of Fire and the Land of Steam in time for a festival celebrating dogs and cats. But Mirai—always on the job—just can’t relax!

Boruto and Konohamaru pay a visit to Remon's village, but are puzzled by Remon's cold demeanor. It turns out that Remon is a descendant of the Souma, a family that has protected the village from goblins for many generations. Thus, she is not allowed to leave the village freely. Furthermore, an important ritual is to be held shortly, so Kankitsu Akitsuki, Remon's childhood friend, imprisons her to prevent her from seeing anyone.

Boruto and Shinki bring Shukaku to Hidden Leaf Village. Upon arriving at the Uzumaki home, Himawari is completely taken with him, but Shukaku finds the entire situation irritating. When told about the day Naruto became the Seventh Hokage—and how Himawari hurt Naruto and Kurama—Shukaku comes up with an idea.

The battle against Urashiki is over, and it's time for Boruto and Sasuke to return to the place where they rightfully belong. Boruto is wistful about leaving Jiraiya and Naruto. Suddenly, Jiraiya makes a request to Sasuke.

Boruto and Mitsuki worry that their mission is in jeopardy, since Kokuri is scheduled to be transferred to Hozuki Castle II. They decide to escape with Kokuri before he's moved. As they discuss their strategy with Sarada, their cellmate Kedama overhears them

Himawari attends the Ninja Academy's trial session where participants get a taste of ninja training. Himawari’s already decided to become a ninja, which annoys Norimaki and Edo, who criticize her for being there just for fun. Things become uncomfortable when they're assigned to the same team.

Team 7 and Mugino manage to evade the gang and continue their pursuit of the culprits. But on the way they encounter a squad of skilled ninja and the situation turns explosive. Amidst the tension they learn intel about the culprits, so the team set out in pursuit, but their way is blocked by Deepa.

Iwabe, Denki and Metal pay a visit to Boruto after he lands in the hospital from overtraining. There, they meet Nattou Nishiki, a young boy who is also a patient. Rambunctious and brash, Nattou easily manipulates the three into getting him an autograph from a certain ninja feared by everyone!

After the Chunin Exams, Katasuke has returned to work at the invitation of the Hokage. Upon seeing him, Boruto becomes annoyed thinking about what happened during the exam. Team 7 is given a mission to escort Katasuke and transport a Scientific Ninja Tool. Stuck on a mission he doesn’t like, Boruto runs into Ao while aboard the Thunder Train headed to their destination.

Wounded and hungry, Kawaki escapes from the tech lab and makes his way to a nearby town to find food. Sumire tracks him down, believing she can help him. Meanwhile, Naruto begins making his way to the area to meet with Kawaki himself.

Kawaki has lost an arm in the battle against Delta, so he is given the prosthetic arm made for Naruto. Though the prosthetic can't move without Naruto's chakra, Naruto shares some of his chakra with Kawaki. Kawaki is surprised by this gesture and remembers how Naruto said that chakra is the power to form bonds with one another. He asks Naruto to train him in Ninjutsu. Meanwhile, Delta informs Jigen that Boruto also has a Karma on his palm. Upon hearing this, Jigen smiles…

Kawaki begins to worry that his presence is endangering everyone in the Leaf Village. Just as he makes the decision to leave, he notices Himawari acting strange.

Naruto and the others are exhausted from their battle with Isshiki. Suddenly, Boruto attacks Sasuke. Momoshiki has taken control of Boruto’s consciousness and stands before them as an enemy. Kawaki desperately calls out to Boruto to snap him out of it. Unfortunately, his words are unable to reach him. Sasuke tells Kawaki a way to bring back Boruto’s consciousness. In order to save Boruto, Kawaki attempts a risky plan using a jutsu he only recently learned. While Kawaki and Sasuke fight a desperate battle, Naruto finally runs out of strength. As his consciousness fades, he and Kurama quietly reminisce about their past.

Team 7, with Sarada as captain, are assigned a mission. Mirai, who was on a mission with Konohamaru, returns to the village critically injured. The mission was supposed to be simple, but Mirai reports that the situation has changed drastically. It’s decided that reinforcements will be sent and Team 7 volunteers to go.

While on the lookout near Dotou Island, a giant mobile fortress appears before Boruto and his friends. Kagura orders Boruto, Kawaki, and Buntan to sneak into the fortress to gather information. Sarada and Mitsuki are able to join up with Denki and the other members of Team 5, and together they begin their plan to save the people of the island.

The main squad led by Funamushi is getting close to the village. Boruto and the others stand by, intending to use traps to slow down the enemy. However, the enemy sees through their plan and they are suddenly thrust into a full-scale battle. Despite being shaken, Boruto and the others fight back. Working together, they are able to handle the enemy’s overwhelming numbers. Even still, Funamushi burns with the desire for revenge and uses a powerful jutsu to corner them.

Cho-Cho and Inojin end up making ramen to help a Rogue Shinobi and ramen shop owner by the name of Shingo Kumano who they met on a mission. They tell him that his ramen doesn’t taste bad, but that it’s missing something. Shingo asks them for advice to make it better. The former ninja takes advantage of his experience to develop a new menu. Will he be able to complete his ultimate recipe?!

Kawaki and Himawari’s class will be putting on a play about the Legendary Sannin for the school festival. The students rehearse wearing prop headbands, but when Eiki discovers that Kawaki brought a real headband, he tries to expose Kawaki’s true identity to drive a wedge between him and Kae. Kawaki can’t afford to let Kae find out about his mission. Will he be able to prevent this from happening?!

As test subjects drop off one by one, Boruto tries to find a way to get everyone out alive. The next experiment is for the subjects to carry candles that are directly linked to their lives. Although some people try to save only themselves, Boruto and a fellow ninja from the Leaf Village, Kiseru Gankubi, aim to clear the challenge together with everyone…but Ouga’s experiment mercilessly pushes them to their limits!

With the disappearance of his Karma, Kawaki has lost his powers. He becomes worried that he won’t be able to protect Naruto or the village he cares for. Seeming to know what Kawaki is thinking, Amado verbally provokes him. Sumire becomes worried that Amado is planning something.

Meanwhile, Code teams up with Eida to get his revenge. Eida introduces him to another person who will be helping them.