Part 1

Opening with a teenaged Boruto Uzumaki facing a teenaged Kawaki in the ruins of Konoha, the former recounts his story.[2] The son of Seventh Hokage Naruto Uzumaki, Boruto feels angry over his father placing the village before his family. At that time, Boruto becomes a member of a ninja team led by Naruto's protégé Konohamaru Sarutobi, alongside Sarada Uchiha, the daughter of Sasuke and Sakura Uchiha, and Mitsuki, Orochimaru's artificial son. Sasuke returns to the village to warn Naruto of an impending threat related to the motivations of Kaguya Ōtsutsuki. Boruto asks Sasuke to train him for the upcoming Chunin exam to impress his father. During the exam, Momoshiki and Kinshiki Ōtsutsuki, the duo whom Sasuke met, abduct Naruto so they can use Kurama, the Nine-Tailed Beast sealed inside his body, to revitalize the dying Divine Tree from the dimension they came from. Boruto, Sasuke and the four Kages, the leaders of other ninja villages, set out to rescue Naruto. The battle ends when Momoshiki, sacrificing Kinshiki to increase his own strength, is defeated by Boruto with Naruto and Sasuke's help; Momoshiki survives long enough to realize Boruto's full potential while warning him of future tribulations and giving him a mysterious mark called "Karma". After recovering from his fight, Boruto decides to become like Sasuke in the future, while entrusting Sarada to follow her dream of becoming the next Hokage.

Boruto and the other learn there is a group called "Kara" searching for people with the marks called Karma. Boruto's team meets Kara's fugitive Kawaki, a boy who also has Karma. Kawaki becomes an adopted member of the Uzumaki family to protect him. However, when trying to protect Kawaki, Naruto and Sasuke are defeated by the leader of Kara, Jigen, who seals Naruto away while Sasuke escapes. Boruto and his teammates save Naruto when Boruto's Karma causes him to be possessed by Momoshiki. After learning of this, Sasuke discovers all Karma users will be taken over by the Otsutsuki clan, including Jigen and Boruto. Meanwhile, a mutiny begins in Kara, with Koji Kashin, a clone of Jiraiya, challenging Jigen, while Amado goes to Konoha to seek asylum in exchange for information, revealing the real leader of Kara as Isshiki Otsutsuki, who has been possessing Jigen ever since he was betrayed by Kaguya when they came to Earth millennia ago, and that Karma allows the Otsutsuki clan to resurrect via the host's body. Although Koji kills Jigen, forcing Isshiki to reincarnate imperfectly while Kawaki's Karma is removed in the process, Isshiki forces Koji to retreat and leaves to attack Konoha.

At Konoha, Isshiki attempts to find Kawaki, but Naruto faces him head-on, preparing to fight. Boruto transports himself and Isshiki to another dimension away from the village, with Sasuke and Naruto following. Since Boruto is Momoshiki's vessel, Isshiki plans to feed him to his Ten-Tails in order to plant a Divine Tree. With Naruto's new power, Baryon Mode, he delays Isshiki as long as possible. After Baryon Mode runs out, Isshiki quickly overpowers Naruto, and finds Kawaki due to the chakra of Naruto's prosthetic arm before teleporting him nearby, but due to lack of life time caused by Baryon Mode, Isshiki dies. Momoshiki uses this as an opportunity to possess Boruto, stabbing and destroying Sasuke's Rinnegan. However, Sasuke and Kawaki fight Momoshiki until Boruto recovers his body, but due to Baryon Mode, Kurama dies.

After being defeated, Isshiki requests Code, who was guarding the Ten-Tails, to carry on the Otsutsuki's will by sacrificing either Boruto or Kawaki and becoming Otsutsuki himself. Code vows to avenge Isshiki, and proceeds to release the two strongest cyborgs created by Amado that were supposed to have been disposed off, Eida and Daemon. The female cyborg Eida agrees to help Code kill Naruto if he in turn spares Kawaki for her to have a normal romance with, because her powers of seduction hinder her from experiencing proper love except with Otsutsuki.

Amado gives Kawaki a weaponized version of Isshiki's Karma. Kawaki uses it to escape from the village. Boruto notices that he can sense his chakra and tries to inform his father, but he does not believe it and talks to the sensors. In order not to lose Kawaki, Boruto has to run after him while the sensors monitor his chakra. Eventually, Code finds Kawaki and Boruto fights him using Karma with Momoshiki's thousands of years of experience. However, Momoshiki takes over Boruto's body, forcing Kawaki to kill him on Boruto's orders. However, Momoshiki revives Boruto as an Otsutsuki, at the cost of his own reincarnation. Both Eida and Daemon are revealed to have been reprogrammed by Amado, and turn on Code, forcing him to flee. In the aftermath, Amado reveals that Eida's and Daemon's powers are shinjutsu transplanted from the corpse of Shibai Otsutsuki, an Otsutsuki who achieved godhood and transcended to another plane. He defines shinjutsu as divine abilities more powerful than ninjutsu which can only be used by gods, including the Karma. Meanwhile, Momoshiki appears in Boruto's mind, showing him a vision of his friends fighting him. Kawaki, having deduced that Boruto, being a full-fledged Otsutsuki, is likely to turn evil, sends Naruto and his wife, Hinata, into another dimension, vowing to kill Boruto and all the other Otsutsukis. Boruto confronts Kawaki, and in the ensuing fight, Kawaki slashes out Boruto's right eye. Sasuke arrives and tries to stop Kawaki, but the latter manages to escape. Kawaki meets with Eida, who uses her Senrigan dojutsu known as Omnipotence to rewrite everyone's memory: Kawaki and Boruto will have swapped places. Only Sumire Kakei and Sarada are immune, with the latter awakening her Mangekyou Sharingan in fear of losing Boruto. Sarada is able to convince Sasuke of Boruto's innocence, with Sasuke swearing to protect Boruto.

Part II: Two Blue Vortex

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Three years later, Sarada has failed to convince Eighth Hokage Shikamaru Nara of Boruto's innocence. The Otsutsuki want the remnant of Uchiha blood, Sarada, and in an attempt to abduct her Code attacks the village with an army of monsters, but Boruto arrives to help fight them off. Shikamaru and the rest of the village are forced to put off dealing with Boruto until they are done fighting Code. Though Boruto defeats Code, Kawaki attacks the former, allowing Code to flee before Boruto can get information about the Ten-Tails from him. Boruto uses the Flying Raijin technique to teleport to the dimension where Code and the Ten-Tails are. The former Kara agent, Koji Kashin, supports him while Boruto sits next to the tree Code has trapped Sasuke in. Boruto then heads back to the village and reunites with Sarada and Sumire, but gets contacted by Shikamaru, who realized that his memories of "Kawaki as Naruto's son" are completely fake after hearing Amado's theory on everyone's memories being altered, with the Mind Body Transmission technique by Ino Yamanaka. Suddenly, Boruto is attacked by Mitsuki. After a small fight, not only does Boruto snap Mitsuki out of his wrath, but he also tells him that his parents, Naruto and Hinata, are still alive. He even reveals the truth about what actually happened three years ago to Shikamaru. Despite discovering the truth, Shikamaru tells Boruto that until they are ready to expose Kawaki's actions to the village, they must work together in the shadows since Boruto is still considered a criminal.

After Boruto informs Shikamaru of the true purpose of the sentient Ten-Tails, Kawaki, accompanied by Delta, goes after him to continue his master plan. Shikamaru discreetly warns Boruto, who quickly makes his escape. Meanwhile, two "Claw Mark" clones named Jura and Hidari invade the village and search for Naruto's whereabouts. But Boruto's younger sister Himawari, who believes her brother is innocent and plans to help him, and Team 10 oppose them. Jura and Hidari begin their assault and try to capture Himawari as their new target. After Koji Kashin locates the attack, Boruto returns to the village and Shikamaru informs him that the two Claw Mark clones are after his sister. Suddenly, Boruto is confronted by Kawaki and both of their Karmas activate, before making his escape. When Himawari and Team 10 escape from Jura, she meets a small Kurama, who tells her that the two of them are one and the tailed beast's component still remain throughout family bloodline after death. To protect Boruto from Kawaki's bloodlust, Shikamaru keeps Kawaki occupied by claiming that Himawari is in trouble, who then heads towards Team 10's location while Sarada and Sumire fight Hidari. As Jura gets the drop on them, he captures Himawari and impales Inojin Yamanaka, causing Himawari to furiously go full power with the chakra of the Nine-Tails. As Inojin's wound heals instantly, Himawari tells Shikadai Nara and Chocho Akimichi to leave with Inojin as she intends to take Jura down. Individually, Himawari, Sarada, Sumire, and Konohamaru try their best to defeat Jura and Hidari, but the two clones easily take them down. Hidari captures Sarada to devour her, but Boruto arrives just in time to successfully rescue Himawari and Sarada.

As they battle against Hidari, Boruto prepares a technique known as Uzuhiko to take down the Claw Mark clone, while Sarada and Konohamaru give him some time. Boruto successfully defeats him, until Kawaki shows up and takes Hidari down to prevent him from escaping and the Claw Mark clone transforms into a thorn soul bulb, which is only way to save Sasuke. Suddenly, Boruto and Sarada get shot by Jura's long-distance attack and retrieves Hidari's thorn soul bulb form.