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...

Boruto's aunt, Hanabi Hyuga, leads an all-girl team made up of Sumire, Wasabi and Namida. They are given a mission to recover animals that someone has released from their cages at the zoo. The team sets out, but Wasabi and Namida start arguing en route, and Sumire is unable to stop them.

Sasuke and the Kage wage an intense battle against the ridiculously powerful Momoshiki and Kinshiki of the Otsutsuki Clan. During that time, Boruto and Naruto, who have always been at odds, face each other and connect for the first time. But Momoshiki interrupts their reunion.

Boruto and Sarada sneak out of the village and head to Orochimaru's research lab to find clues about Mitsuki. After evading the ninja guarding the entrance, they get in. But what they observe at the facility and hear from Orochimaru makes Boruto realize that he never truly knew Mitsuki. Meanwhile, the village finds out that Boruto and Sarada have gone in search of Mitsuki, and Shikadai and his Team 10 are assigned a tracking mission to bring back them back.

Boruto and his friends decide to go the Hidden Stone Village to see the former Tsuchikage, Ohnoki. In case of an emergency, Inojin stays back with the young Akuta, who is attached to him. The team secretly enters the village determined to find Ohnoki, but they are unaware that they are being watched.

Boruto comes across an eating contest, held by the popular eateries in the Leaf for Parent and Child Day. Many families participate but they don’t know that this event has an outrageous hidden motive arranged by the organizers…

Boruto and Sarada confirm Juugo’s appearance. However, Juugo is under the influence of a ‘Cursed Seal’, and has transformed into a ferocious monster. The ‘Cursed Seal’ is one of Orochimaru’s research materials. Even though it amplifies strength and stimulates that attack instincts of living beings, Juugo is someone who possessed that capability from birth. Juugo has lost control over himself and begins to attack, putting up a difficult fight against Boruto and his comrades. Even though he’ll be getting assistance from his friends, will they cause damage to Juugo somehow?!

Konohamaru’s cousin, Mirai Sarutobi, is assigned to escort the Sixth Hokage Kakashi and his friend Might Guy to the hot springs.

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.

Urashiki is determined to get Shukaku's chakra and attacks ruthlessly. Boruto and Shinki form a united front and unleash each of their special jutsu. However, Urashiki proves to be a formidable opponent that neither Sasuke nor Gaara could defeat. Will Boruto and Shinki be able to find a way to counter him?

Urashiki appears to steal the chakra of Nine Tails from Naruto, but his attempt is unsuccessful. In order to save Naruto, Boruto, Sasuke and Jiraiya pursue Urashiki. Jiraiya then notices that the malevolent Nine Tails Chakra has started filling the air.

Inojin approaches his parents about mastering the Mind Transfer Jutsu. Cho-Cho agrees to assist and everything is set for training to begin. With his father Sai observing, Inojin starts training with Ino. But due to his lack of confidence, Inojin's unable to execute the jutsu, which ends up irritating his mother.

After completing his mission to guard Tento, Boruto is assigned a new B-rank mission with Sarada and Mitsuki. Boruto is excited to start but he finds the rare X Card that he had wanted in his pocket. Realizing that this was from Tento, he goes to their hotel and learns that Tento's life is in danger.

Using intel obtained from Shojoji the leader of the Mujina Gang, Sai and Sasuke journey to the Hidden Rain Village to find a location thought to be the hideout of an organization known as "Kara, the Husk.

Under Kakashi's watchful eye, Boruto succeeds in powering up his own style of Rasengan. And he demonstrates his progress in a battle against an opponent of Kakashi’s choosing. Meanwhile, Sasuke and Sakura switch places to train their daughter. With firm resolve, Boruto and Sarada continue their training and begin to see the results of their hard work.

Boruto and Sarada rush to Victor's research lab where they find a horrifying plant stealing the chakra of the people near it. As they work with Konohamaru to try to bring it under control, Deepa appears!

Boruto, Sarada and Mitsuki are assigned to carry out Team 7’s missions by themselves until Konohamaru returns from an unexpected assignment. Boruto runs into Mugino in town and ends up going to his home at Mugino’s invitation.

Boruto and the others return to the technology lab to contain and watch over Kawaki while Konohamaru returns to the Leaf Village to report the events of the mission to Naruto.

Delta uses her destructive beam that can neutralize any regenerative power. Undaunted, Naruto forcefully suppresses it with a Giant Rasengan. He then turns up the power of his jutsu and propels it towards Delta. Unfortunately, Delta has been fitted with Scientific Ninja Tools and is able to absorb any jutsu, no matter how powerful… What will be the outcome of this battle?!

Koji Kashin continues his battle with Jigen, whose body is revealed to have been taken over by Isshiki Otsutsuki. He continuously hits Jigen with a barrage of attacks in an attempt to drag Isshiki out of his body and destroy him.

In order for Kawaki to become a genin, it’s decided that he can take a special test that differs from the one held at the Ninja Academy. A D-rank mission is deemed to be equivalent, so Kawaki is assigned as an additional member. However, he is difficult to work with, ignores the need for teamwork, and acts on his own—giving his teammates a hard time while disrupting the mission!

The Land of Water is taken over by pirates, and contact with Denki's Team 5 is lost. The new Team 7 joins up with a unit led by Kagura and sets out for Dotou Island to assist Team 5 and rescue the islanders. However, the unit is made up of Buntan, Hebiichigo, and Kyoho, who in the past had called themselves the “New Seven Ninja Swordsmen of the Mist.” Sarada and Mitsuki go ashore to scout the island while Boruto and the others stay back and watch the situation nearby.

Denki and Iwabe protect the village children who accompanied them but they are captured by Funamushi and his squad. Funamushi’s squad shows up once again to attack the village. Funamushi burns with the desire to avenge Seiren as he fiercely battles Boruto and the others once more.

Kawaki enrolls at the Ninja Academy and begins classes as a freshman with Himawari and the others. But it’s actually a secret mission to protect a princess from assassins. This is kept a secret because she’s come from abroad to study. Since it is a personal request from Naruto, Kawaki decides to attend the academy hesitantly, where the students are younger than him. Kawaki’s difficult school life with an unreliable teacher named Hana Kaka and his unique young classmates begins!

While Boruto and the others are forced to participate in Ouga’s experiments, Sarada and her team investigate Boruto’s disappearance and discover the existence of a suspicious individual.

Meanwhile, Boruto is shocked to discover the identity of someone who may be working for Ouga. Just then, a test subject is found dead—killed for reasons that have nothing to do with the experiment.