Kaguya Otsutsuki. Mother of Hagoromo Otsutsuki: the Sage of the Six Paths, Hamura Otsutsuki, Black Zetsu, Grandmother of Indra and Asura Otsutsuki's, and Progenitor of the Kaguya, Senju, Uzumaki, Hyūga, and Uchiha Clan's, and the Byakugan, Sharingan

Throughout the world, people's chakra is drained and channeled through the roots of the God Tree. The chakra is absorbed into Madara, transforming him into Kaguya. Kaguya senses the Yin and Yang powers in Sasuke and Shisui, and flings them away with her hair. She confirms with her Byakugan that they are reincarnations of Asura and Indra, her Grandchildren. Kakashi asks Kaguya her intentions, but she deems it pointless to explain to shinobi who tamper with chakra, ignorant of its meaning. Not wishing to damage the world with more fighting, Kaguya teleports everyone, including herself, to a lava-filled dimension. While she hovers above, Shisui, Naruto, Sasuke, Kakashi, and Sakura begin falling towards the lava. Sasuke saves himself by summoning Garuda to fly on it, then has Garuda catch Naruto. Kakashi, and saves himself by pinning one end of an opened scroll to a wall with a kunai and hanging onto the other end of a rope. while Shisui uses god technique to save himself and Sakura.

Kakashi then surmises that they aren't in a genjutsu, but in an entirely different dimension. Shisui explains to Sasuke that they must not be killed or else the world will end because only they can seal Kaguya away. Suddenly, Kaguya seizes the moment by shooting hair needles at them. Sasuke activates Susanoo, blocking most of the hair needles, but a few strike Garuda's tenketsu, causing them all fall. Shisui uses god technique again to bring the rest up to him and Sakura. Intent on reuniting chakra once again, Kaguya releases a wave of chakra fists. Shisui manages to briefly counter her attack, but is overpowered, however, it creates an opening for Sasuke to attack with his Susanoo. Kaguya counters his attack, shattering Susanoo. After Sasuke teleports to Shisui, Shisui creates a floating platform from a Truth-Seeking Ball for Sasuke. Kaguya then appears behind Shisui and Sasuke and paralyzes them as they turn to see her crying face. As Kaguya thinks of her sons, Black Zetsu manifests from her and begins covering them and absorbing their chakra. Black Zetsu tells them about his role as Kaguya's will and as a manipulator of the history of shinobi from the moment he was born, just as Kaguya was first sealed.

Kaguya voices her hatred for her sons. Outraged by Black Zetsu's claims, Naruto frees Shisui and Sasuke, disagreeing with him about those whom shaped shinobi history and how Mother's should feel about their children. Sasuke surmises they need to create an opening to seal Kaguya, Naruto decides to use a certain Jutsu, and starts filling Sasuke in on it. Black Zetsu dismisses them, pointing out Kaguya can absorb all Jutsu. From afar, Sakura observes them, relaying the information to Kakashi, who is still in awe of Kaguya's power. Sasuke is doubtful about Naruto's strategy involving a Jutsu he practiced in secret even more than the Rasengan but agrees to try it. He engulfs Kaguya with Amaterasu, which she effortlessly absorbs. Naruto moves in and transforms into a group of naked men, stunning Kaguya. Sakura is irate that Naruto would try that on someone so powerful, but is shocked when Shisui who was discised as one of the naked men. lands a hit on Kaguya. Kakashi wonders if Jiraiya is watching Naruto save the world with perverted ninjutsu. Sasuke teleports Kaguya between himself and Shisui, almost making physical contact, but Kaguya teleports everyone to her ice dimension, locking them in place with ice.

Naruto, Sakura, and Kakashi discuss Kaguya's Jutsu. Kaguya escapes the ice and moves in to absorb their chakra again. Sasuke frees himself and Shisui with Amaterasu and Kagutsuchi. At Black Zetsu's suggestion, Kaguya splits them up, throwing Sasuke in her desert dimension. Shisui tries to keep the portal open, to no avail. Shisui evades Kaguya, who causes the surrounding landscape to attack Shisui. Sasuke wanders through the desert dimension. before finally allowing himself be captured to draw Kaguya out. Shisui use god Technique to teleport Sasuke behind Kaguya. Sasuke launches an attack on Kaguya, severing her left arm but she shifted to dimensions once more Noting that this time he would be the distraction, Sasuke engages Kaguya giving her no time to relent as he dons his Complete Body — Susanoo and flies towards her.

Sasuke servers Black Zetsu from Kaguya and immobilizes him. Kakashi laments his powerlessness and thinks back to his failures. Elsewhere, Obito asks Rin to wait a bit longer, as he wishes to aid Kakashi. Obito's chakra rises from his ashes and envelopes Kakashi. Reunited, Obito reminds Kakashi to not follow him to the afterlife anytime soon, and tells him to become the Sixth Hokage, in which he gives him an "early promotion gift". Kaguya knocks Sasuke back, and Shisui attacks her with his enhanced Rasenshuriken, resulting in Kaguya undertaking an unstable Tailed Beast transformation. The beast's hands begin attacking, and when they aim for Sakura, she is saved by Kakashi's Susanoo. As he joins the fight, Kaguya creates a gigantic Truth-Seeking Ball and reemerges. Kakashi uses his new found techniques against Kaguya. Shisui and his clone faces her, and when Kakashi warps away Black Zetsu's attack, Sasuke swaps with the clone as Sakura punches her. Shisui Naruto and Sasuke make physical contact with Kaguya in order to seal her. activating the fūinjutsu taught to them by Hagoromo. As her Rinne Sharingan is obscured, Kaguya wonders how scattered pieces of her chakra were able to seal her again.

Kaguya's Expansive Truth-Seeking Ball begins crumbling, the land begins sealing Kaguya, and Kaguya herself begins reverting into the Demonic Statue of the Outer Path, as the tailed beasts are separated from it. The rabbit head left in it spits Madara's body out. Shisui, Sasuke, and the tailed beasts meet up with Kakashi and Sakura, while Naruto goes looking for Black Zetsu, who is already intent on scheming Kaguya's next resurrection. Naruto denounces Black Zetsu's role in shinobi history, and throws it toward the forming moon, sealing it as well. Naruto meets up with the others, and Sakura wonders how they'll get out of Kaguya's dimension. Hagoromo summons everyone back with the aid of the previous Kage he called from the Pure Land. Hagoromo congratulates Kakashi on coordinating the sealing, though Kakashi downplays his role. Kakashi bids Obito farewell as Obito's chakra in him fades away. Hagoromo stops Sasuke from reaching Madara, who is about to die. Madara and Hashirama exchange their final words as Madara dies. Hagoromo announces he'll release the summoned Kage, including the ones from Impure World Reincarnation. Minato wishes Naruto happy birthday as dawn breaks. Naruto motormouths several things for Minato to tell Kushina as the Kage's spirits are released and go back to the afterlife.

The tailed beasts make plans on where to go. Hagoromo asks Kurama to return to Naruto and for Matatabi to fully return to Shisui, who due to having a bit of each of their chakra, can act as a gathering place for the tailed beasts to communicate, Hagoromo also asks that Son Gokū, Saiken, Chomei, and Shukaku Join Shisui while Kokkuō and Isobū joins Sasuke. Hagoromo explains that Shisui and Sasuke, having the tailed beasts' chakra and the Rinnegan, can release the Infinite Tsukuyomi. Sasuke wants to kill the Five Kage before releasing the Infinite Tsukuyomi, to everyone's surprise and puts the tailed beasts under genjutsu, also planning to kill them later. Shisui apologizes to Hagoromo. Kakashi questions Sasuke's motives. Sasuke explains that while vengeance and destruction were his initial goals, now he wants to destroy the shinobi world as it is to rebuild it anew, blaming the Five Kage for how the world has become. Sasuke traps the tailed beasts with Chibaku Tensei. Sasuke is intent on killing Naruto, planning to use the captured tailed beasts to release the Infinite Tsukuyomi later. When Naruto opposes him, Sasuke tells Naruto they need to fight somewhere else. Hagoromo tells Kakashi about his sons and he believes Naruto can still save Sasuke.

Shisui, Sakura, and Kakashi arrive at the edge of the destroyed Valley of the End and spot Naruto and Sasuke on the ground. Shisui and Sakura jumps down and begins healing their arms. Naruto thanks them. Sasuke at first tells Shisui not to bother with him, but when Shisui tells them she needs to focus, a guilt-ridden Sasuke apologizes for what he has done, Sasuke reflects on his and Naruto's paths. The roots of the God Tree wither, and the victims of the Infinite Tsukuyomi are freed, Naruto and Sasuke performing the hand seals together with their remaining hands. Sasuke frees the tailed beasts.

Back in Konoha, a funeral is held for those who died, including Shikaku and Inoichi. Sometime later, several thousand people flock to Konoha to see Shisui, most or them girls. Tsunade congratulates Kakashi on succeeding her as Hokage, dismissing his concern about the great amount of paperwork, pointing out if she managed it, so would he. Sasuke is held prisoner, bound in a full body jacket, and seals over his eyes. Kakashi and Shisui visit Sasuke in prison. The next day, Sasuke is free, his plea and contributions for ending the war warranting him a pardon. Sasuke wants to see the world by himself to atone and grow as a person. Sakura asks him to wait until his artificial arm is ready but he declines it. Naruto goes to see Sasuke as he leaves and hands Sasuke his scratched forehead protector, which Naruto kept all these years.

But now Shisui and His girlfriends have decided to split up for good. Sakura begins a relationship with Sasuke, Ino with Sai, Temari with Shikamaru, Hinata goes back to her crush on Naruto, Tenten starts a Relationship with Aroi Kraigen, Asher Haizen Starts a relationship with his former girlfriend Aria Ozie, Kurenai Raises her and Shisui's Daughter as Mirai Sarutobi, the daughter of Kurenai and Asuma. Meanwhile there are other relationships going on Sakumo Hatake the Second and the Fifth Mizūkage get married, Asuma Sarutobi II marries Samui of the Hidden Cloud, while her teammate marries Chōji, leaving their third Teammate Omoi to become the Fifth Raikage's Bodyguard. Shisui himself starts a long distance relationship with Kūrõtsūchi Kamizuru, who eventually becomes the Fourth Tsuchikage.