Another intense battle begins for Boruto, Sasuke and Jiraiya as they try to defend Naruto from Urashiki. Sasuke protects Naruto, allowing Boruto and Jiraiya to barely escape with him.

Sumire's wish comes true and she joins the Scientific Ninja Tools Team, leaving only Wasabi and Namida on Team 15. A new member, Tsubaki Kurogane, a young girl who hails from the Land of Iron, joins them.

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.

The clock ticks down to the rendezvous time for the escape, but there's no word from Sarada. If they miss this chance, everything will be ruined. Boruto puts his faith in Sarada and proceeds as planned with Mitsuki and Kokuri. Meanwhile, Sarada's lost consciousness from falling to the underground level of Hozuki Castle.

One rainy night, guided by Mikazuki the cat, Mitsuki rescues an injured man. Mysteriously, Mikazuki seems to take a liking to the man who says he’s come to visit his sister who works in the Leaf Village. Soon after, Team 7 is assigned to back up the Leaf Police Force on a security mission. Their client is a president of a company who is being targeted by a serial killer known as "The Rainy Day Killer.

Boruto and the team finally catch up to the real thieves, two ninja brothers from the Land of Kasumi. Yuga uses a Forbidden Jutsu to summon a monster, and seals it and the team inside a strong barrier. Naruto insists on defeating it and getting out of the barrier. But Mugino argues that unnecessary fighting should be avoided since they don't know how to counter this special jutsu.

Boruto and Sarada convalesce at the Leaf Hospital while Mitsuki returns to Orochimaru's for treatment. For Boruto and Sarada, their inability to fight back against Deepa turns from frustration to resolve. Meanwhile, Konohamaru gives the Hokage his report regarding the incident, and in order to investigate the connection with the Kara more thoroughly, he asks that he be allowed to conduct surveillance on Victor's company.

Shikadai comes to see Boruto in the midst of training and witnesses his friend's determination to break through his slump. Shikadai, who also experienced Deepa's frightening power, tells Boruto that a rematch with Deepa would be reckless. Boruto explains his real reason for wanting to become stronger, and asks for Shikadai’s help. Meanwhile, Sarada trains with Sasuke to hone her Sharingan, but Sakura worries about her well-being.

Separated from Boruto and Sarada, Konohamaru battles Victor. But someone unexpected shows up to fight alongside him. Meanwhile, Boruto and Sarada are trying to defeat Deepa to even the score, but he still proves to be a formidable opponent despite all of their training.

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.

Team 7 has arrived at a high-tech research center along with Katasuke. There, they end up running into some familiar faces. The mission has ended without incident, and Boruto is ready to head home. However, there’s more they must do. Boruto and his friends end up cooperating in a test-run of a Scientific Ninja Tool that is under development. Boruto is unhappy at first, but as the test run continues his feelings start to change. As that happens, Team 7 is given a new urgent assignment from the Hokage.

The showdown between Team 7 and Ao begins. Team 7 works together to bring Ao down with various attacks and jutsu, but he proves to be a difficult adversary due to his use of scientific ninja tools.

Boruto and the others learn that the boy named Kawaki is the target that Kara has been seeking. They watch on as a battle rages between Kawaki and the Kara Outer, Garo, and are shocked by the young man's capabilities.

Kawaki collapses and is tormented by nightmares from his childhood. As a child, Kawaki endured an abusive father, until one day a man appeared before him— none other than Jigen, the leader of Kara.

Kawaki goes into town with Naruto to get a new vase to replace the one that he broke. On the way to the Yamanaka Flower Shop, they are joined by Sarada. Unaccustomed to peaceful everyday life, he snaps at Sarada’s attempts to talk to him, and almost attacks a child for bumping into him.

Delta forces her way into the Leaf Village to take Kawaki back and appears before Boruto and the others. Naruto confronts her to protect Boruto, Himawari and Kawaki. She attacks Naruto with Scientific Ninja Tools that have been implanted into her heavily modified body. In response, Naruto unleashes the power of the Nine Tails, and a fierce clash ensues!

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.

Naruto has been pulled into a different dimension by Jigen. There he encounters Sasuke, who tells him that Jigen is a dangerous person and that they must do whatever it takes to defeat him immediately. Naruto and Sasuke work together to defeat Jigen in a fierce battle, but they struggle against Jigen's advanced fighting abilities and mysterious jutsu. Meanwhile, Boruto gets a bad premonition when his Karma starts acting up, and so he quickly returns home with Mitsuki. Kawaki and Sarada are there, worried about Naruto's safety.

The reformed Team 7 launches a series of attacks on Boro. But even when they land successful attacks, Boro instantly revives himself with his extraordinary regeneration powers.

Konohamaru and Sai are given a mission to infiltrate Boro's cult in order to obtain information on Kara and its whereabouts.

Amado reveals to Naruto and the others the knowledge that he possesses regarding Jigen, the Otsutsuki Clan, and Karma. Meanwhile, Koji Kashin confronts Jigen, and Amado's plan to eliminate him is revealed.

Boruto opens a portal and transports Isshiki and himself to another dimension. Naruto and Sasuke follow them, and the final battle against Isshiki begins.

The match between Sarada and Cho-Cho begins. Kawaki has been invited by Naruto to observe, as well as Shinki and others who have come from the Hidden Sand Village. Who will emerge victorious in a battle between best friends?!

As Sarada and the others hurry to evacuate the people of the island, Boruto grows anxious when he learns they are being threatened by the mobile fortress, which is equipped with a powerful weapon. Kagura, Hebiichigo and Kyoho show up to assist Boruto, Kawaki and Buntan. Together, they do what they can to destroy the weapon to protect their friends, but they are obstructed by Tenma and are forced to fight him.