The ninja assigned to the Hidden Leaf Gate are attacked, and Mitsuki disappears. Boruto and Sarada are unaware of this when their scheduled mission is suddenly canceled. Worried, the two start searching for their teammate. When they learn that all the jonin have been summoned by the Hokage, they set out to find out what's going on.

Kokuyou confronts Boruto and the others. Kokuyou, whose only goal is to become strong, is so powerful that he's taken down the Leaf ninja pursuing Mitsuki. He easily drives Boruto and his team into a corner. Just then, backup appears. Boruto and his friends manage to overcome Kokuyou, and finally catch with up Mitsuki.

In order to get out of the barrier, Boruto desperately searches for his heart of stone, but he has little success. Then he encounters Sekki, one of the Genbu Three that participated in the recent Chunin Exams. Sekki has also come to the training ground in order to find his heart of stone. Seeing their predicament, Ohnoki tries to help them.

Boruto and Sarada are caught and taken back to the Hidden Stone headquarters along with Ohnoki. There, they find that Ku and his supporters have taken the village, and that things have changed drastically. Kokuyou and Kirara swoop down on Boruto and Sarada, but Shikadai comes to the rescue!

Sustaining great damage from Mitsuki’s attack, Ku flees the scene. Boruto and Sarada attempt to chase after him, but Kirara blocks their path! Meanwhile, Sekiei watches everything unfold. Shocked and confused by the actions of Mitsuki, Sekiei recklessly attacks him. Not wanting to fight, Mitsuki tries to stop him.

Ku appears once again to provoke and attack Boruto. Meanwhile, reevaluating his true will and intent, Ohnoki prepares for a fight to the death in order to stop Ku from doing any more harm.

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.

Mirai leaves the inn with Tatsumi without telling Kakashi and Guy. At the hot springs Mirai thinks she sees her father Asuma, but something feels off. Will Mirai be able to get back to her escort mission in one piece?

One day, Boruto and Konohamaru rescue Remon Yoimura from an attack. Remon says she has come to Hidden Leaf Village for sightseeing. Boruto and Konohamaru offer to show her around the Leaf and provide some protection as well.

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.

Boruto manages to reach Sasuke, but he sees his mentor disappear before his very eyes due to an attack by Urashiki Otsutsuki. It turns out that Sasuke, along with the Kazekage and Shinki, was in the middle of battling Urashiki, who was pursuing Shukaku, the One Tail. Gaara uses a Sealing Jutsu and manages to stop Urashiki, but he believes it’s only a matter of time before the jutsu is broken. He orders Shinki and Boruto to go to the Leaf Village to keep Shukaku safe.

Boruto is forbidden to participate in the counterattack on Urashiki because he was previously targeted by the Otsutsuki. Frustrated by this decision, Boruto argues with Naruto when a report comes in that Urashiki has been located.

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.

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.

Boruto has a dream about the day he defeated Momoshiki Otsutsuki. It ends up bothering him so much that he can't focus on his mission. He then meets Tento, the son of Ikkyu Madoka—the Feudal Lord of the Land of Fire—who’s in the Hidden Leaf for a meeting with the Hokage.

Tsubaki, Sumire’s replacement on Team 15, is proud of her samurai upbringing and is highly skilled, but her team’s overall mission performance is lackluster. Tsubaki devises a plan to hone her team’s skills, where they fight for who performs best on missions.

Boruto and the team finally find the missing researcher. Despite his resistance, the team is determined to take him back safely to their client.

Boruto and the team are determined to reach Asaka, the eldest brother of the Land of Silence Ninja, before Deepa does. They catch up to him, but Deepa arrives soon after and attacks ruthlessly. They try to counter, but nothing seems to work. In the midst of their panic, Victor appears!

Konohamaru and Mugino continue keeping their eye on Victor's company. They receive intel that the Feudal Lord of the Land of Valleys will be touring the company, giving them the opportunity to check the inner reaches of the secretive facility. Meanwhile, Boruto and Sarada complete their training and visit the woman who requested their previous mission.

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!

After finding out that Konohamaru and Mugino have gone missing, Team 7 is ordered to go to their last known location and investigate what happened. Team 7 and Katasuke arrive at the airship wreckage, but are attacked by strange puppets.

As Naruto sleeps, Kawaki repairs the vase he broke. Suddenly, Kurama, the Nine-Tailed Beast, appears before him. Kurama has been living with Naruto since he was sealed within him and tells Kawaki that Naruto used to be just like him. Upon hearing about Naruto's life, Kawaki aspires to become just like him. He reaffirms his decision to work with Boruto, who is also branded with a Karma, to defeat Jigen and the Kara.

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.

Naruto and Sasuke are greatly overwhelmed by Isshiki's abilities. As a last resort, Kurama offers Naruto a chakra mode called Baryon Mode, which grants him immense power. The intensity of this power, however, could end his life.

One after another, the winners of the finals are being decided. Only a few matches remain, but Boruto and Mitsuki still have not appeared at the venue. Sarada worries that at this rate, the duo will be disqualified. Meanwhile, the next match is between Denki and Tsubaki.

The new Team 7—with Kawaki its newest member—is assigned to escort Katasuke to a ceremony in the Land of Water. Boruto is looking forward to seeing Kagura Karatachi, a shinobi from the Land of Mist whom he hasn't seen since their Academy field trip to the Land of Water. However, in the shadows of the ceremony, a group harboring a grudge stealthily begins to make its move.

As Boruto and the others ready their plan, they learn that one enemy unit is heading to the village ahead of the rest. Since they haven’t finished making preparations, the village will be in danger, so they hurry to evacuate everyone. Kagura worries that they won’t have enough people to fight. Just in case, he releases the curse placed on Buntan, Hebiichigo, and Kyoho, temporarily setting them free. Hesitantly, they agree to fight alongside Kagura and Boruto.

Boruto and his friends manage to triumph over Funamushi, but they aren’t able to savor the victory. Everyone is having a difficult time believing Denki and Iwabe are still alive days after being captured. Meanwhile, Boruto discovers a hidden side of Funamushi when he is targeted by people who looked up to the pirate, as revenge begets more revenge. Boruto has always continued to push forward until now, but this causes him to question the point of fighting.

Araumi is furious about the loss of family members and many of his subordinates during the battles so far. He officially declares war against the Land of Water. Upon hearing this, Mizukage decides to fight him to the bitter end. As war between the Land of Water and the pirates becomes inevitable, Boruto is confused by Ikada’s decision to fight the Land of Water. He does everything he can to prevent any more casualties, and Sarada and Mitsuki assist him in his efforts.

While strolling through the village, Kakashi and Boruto come across some people arguing. Boruto sees a gloomy-faced young couple and learns they’re engaged, and that their grandfathers are feuding. For the sake of their future, Boruto wants to help them out and asks Kakashi for advice, but Kakashi is totally uninterested. However, something seems to sway Kakashi and he decides to help…

Kawaki and Himawari participate in a training session in the forest near the academy. The class is split into three-person teams and Kawaki ends up on a different team from Kae. Anxious about losing sight of Kae, Kawaki is unable to focus and ends up burdening his assigned team. Kae is lured away by a mysterious person and disappears. Fearing that she is in danger, Kawaki and Himawari rush to find her.

The assassin targeting Kae has finally been revealed. Because of their previous clashes, Kawaki knows they are a powerful foe. He decides to chase after the assassin by himself to prevent putting any more students in danger. But Kawaki finds it difficult to do that without knowing where the assassin is; what’s more, his classmates desire to work together to chase down the assassin and save Kae. And so, the entire class begins their pursuit!

While everyone is exhausted from Ouga’s experiments, a test subject talks about their goals, which leads everyone to talk about what they want to do if they survive. The mood is lightened, but Ouga begins a new experiment. Due to the careless actions of certain test subjects, everyone's lives are in danger once again.