Part I: Naruto Next Generations
A teenaged Boruto Uzumaki faces off against a teenaged Kawaki in the ruins of Konoha, the former recounts his story.[2]
The son of Seventh Hokage Naruto Uzumaki and his wife Hinata Uzumaki, and older brother of Himawari Uzumaki, Boruto feels so angry over his father placing the village first 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 Uchiha and his wife 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 Fox 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 a vigilante like Sasuke in the future, while entrusting Sarada to follow her dream of becoming the next Hokage.
Boruto and the others learn about 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. 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. Sasuke discovers all Karma users will be taken over by the Ōtsutsuki clan, including Jigen and Boruto. Meanwhile, a mutiny begins in Kara, with Koji Kashin, a clone of Naruto's late master Jiraiya, challenging Jigen, while Amado goes to Konoha to seek asylum in exchange for information, revealing that the true leader of Kara is Isshiki Ōtsutsuki, who has been possessing Jigen ever since he was betrayed by Kaguya when they came to Earth millennia ago, and that Karma allows the Ōtsutsuki 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. 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 and destroy Sasuke's Rinnegan. 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 Ōtsutsuki's will by sacrificing either Boruto or Kawaki and becoming Ōtsutsuki himself. Code vows to avenge Isshiki's death 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 Ōtsutsuki. Amado gives Kawaki a weaponized version of Isshiki's Karma. Kawaki uses it to escape from the village, but Boruto notices that he can sense his chakra. In order not to lose Kawaki, Boruto has to run after him while the sensors monitor his chakra. Code eventually 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 in front of Naruto. Momoshiki revives Boruto at the cost of his own reincarnation, causing Boruto to become a full Ōtsutsuki. Eida and Daemon were revealed to have been reprogrammed by Amado, and turn against Code, forcing him to flee.
Amado reveals that Eida's and Daemon's powers are shinjutsu transplanted from the corpse of Shibai Ōtsutsuki, an Ōtsutsuki who achieved godhood and transcended to another plane. He defines shinjutsu as divine abilities more powerful than ninjutsu, which can be used only by gods, including the Karma. In the aftermath, Momoshiki appears in Boruto's mind, showing him a vision of his friends fighting against him. Kawaki, having deduced that Boruto, being a full-fledged Ōtsutsuki, is likely to turn evil, sends Naruto and Hinata into another dimension, promising to free them after killing Boruto and all the Ōtsutsukis. In the ensuing fight, Boruto confronts Kawaki and loses his right eye protecting Sarada. Sasuke arrives and tries to stop Kawaki, but Momoshiki helps the latter escape. Kawaki meets with Eida, who activates her Senrigan dojutsu known as the Omnipotence to rewrite everyone's memories: Kawaki and Boruto permanently swapped places, with Kawaki forcing Eida to lie that Boruto has killed Naruto and Hinata. Only Sumire Kakei and Sarada are unaffected by the Omnipotence, with Sarada awakening her Mangekyou Sharingan and is able to convince Sasuke of Boruto's innocence. After Eida apologizes for her actions, Boruto vows to regain everything taken from him. The story ends with Kawaki keeping Naruto and Hinata sealed away permanently as the world believes that Seventh Hokage is dead.
Part II: Two Blue Vortex
Three years have passed, Naruto and Hinata are still alive and unconscious in Kawaki's dimension, while Sarada has failed to convince the Eighth Hokage Shikamaru Nara of Boruto's innocence. Code attacks the Konoha village with an army of monsters, but Boruto arrives to fight them off. Kawaki attacks Boruto and allows Code to escape before Boruto can get information about the Ten-Tails. Boruto uses the Flying Raijin technique to teleport to the dimension where he encounters Code and the four Shinju clones. After escaping, Boruto is supported by Koji Kashin, who became his new mentor, while sitting next to the tree that Code has trapped Sasuke in. Boruto reunites with Sarada and Sumire in the village, but Mitsuki attacks Boruto. After snapping Mitsuki out of his wrath, Boruto reveals the truth about what happened three years ago to Shikamaru through the Mind Body Transmission technique by Ino Yamanaka. Shikamaru tells Boruto that until they are ready to expose Kawaki's crimes 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, two Shinju clones Jura and Hidari arrives to the village to search for Naruto's whereabouts. Himawari, who believes that Boruto is innocent and wants to help her brother, steps forth to oppose them. The two Shinju clones begin their assault and Jura attempts to capture Himawari as their new target, as she is revealed to be Kurama's new host, while Sarada, Sumire and Konohamaru fight Hidari. After failing to obtain the Thorn Soul Bulb (which was the key to save Sasuke), Boruto was arrested and interrogated but manages to escape.
