You meet Hagoromo Otsutsuki?

Shisui was brought before Hagoromo Otsutsuki the Sage of the Six. Hagoromo tells Shisui of the cycle of reincarnation of the Sage's sons, Indra and Asura, and tells Shisui of the great abilities of Indra, especially in comparison to that of the younger brother. When Shisui recognizes these traits in himself, Hagoromo reveals to him that he is the reincarnation of his oldest son Indra Otsutsuki.

He asks Shisui if he can guess who Asura's reincarnation is, and Shisui correctly concludes it is Sasuke. At the same time, Hagoromo has the same conversation with Sasuke, revealing his status as Asura's reincarnation, and having him realise Shisui is Indra's. Hagoromo goes on to explain that Hashirama and Madara are the previous reincarnations, and that by taking Hashirama's power, Madara recreated Hagoromo's chakra, awakening the Rinnegan, despite leaving Indra's descendants instructions against it, similarly Shisui's Father's own Father and Mother were the younger siblings of Both Previous Reincarnations and As a result of this Zaskuare's Senju and Uchiha Blood gave him ascess to the Rinnegan in both of his eyes and passed this down to Shisui, albeit with only one Rinnegan activated upon Birth. Shisui being Born with Senju Blood inherited from his Father as well as his Father's Uchiha Lineage Meant that he Inherited Hashirama and Asura's Wood-Style and the Rinnegan from his father, and by extension Indra. Hagoromo goes on further to state as the first Reincarnation to naturally possess both Brother's Chakra from birth, he has practically limitless Potential, and has the Ability to use any Jutsu regardless if it is Clan-Specific.

Hagoromo asks that Shisui Become the new Patriarch of the Otsutsuki Clan of Earth since he and Hamura are entrusting their Legacies to him.

Hagoromo also explains that his mother Kaguya used her powerful dōjutsu to rule over humanity, and that Madara is on his way to acquiring that same power. Hagoromo asks Shisui to stop Madara, who accepts his request. The chakra of the tailed beasts converge, and Hagoromo notes the prophecy he heard long ago has come true. Hagoromo asks Sasuke to cooperate as well, and entrusts both Shisui and Sasuke with his powers, Hagoromo Also Entrusts Shikotsumyaku, Sakon and Ukon's Kekkei Genkai, Jūgo's Clan's Kekkei Genkai, and the Rinha Clan's Kekkei Genkai. Hagoromo tells the Two cousins to Continue to battle with the Reincarnated Hokage. Having survived and being impressed by Guy's Evening Elephant, Madara asks Guy to keep on fighting him, deeming him the strongest taijutsu user he has ever faced. Guy prepares to use his last technique while Shisui and Sasuke awaken. As Guy prepares the Night Guy, Kakashi recalls his father's accurate prediction of Guy's potential when they were children. Guy's powerful kick lands on Madara, through the Shinju, almost killing him. Guy's body begins to disintegrate and an elated Madara, regenerating from the attack, attempts to finish him with a Truth-Seeking Ball only for Shisui to kick it away, much to his surprise. as Shisui appears with a newly awakened second Rinnegan.

Madara is puzzled by Shisui stopping Guy's chakra from fading. Madara defends himself from Shisui's punch with his remaining Truth-Seeking Ball, noticing an incomprehensible and Incalculable increase in Shisui's power. With Son Gokū's chakra, Shisui creates a lava Rasenshuriken and attacks Madara and the tree with it, dodging Madara's Limbo: Border Jail. Shisui's attack severs the tree, which appears to tell Madara to absorb it, which Madara does. Shisui takes Guy to Lee and Gaara. meanwhile, Sasuke frees Tobirama from Madara's black rods, Tobirama notices a change in him, and Sasuke asks if Tobirama can teleport him. Madara recovers from having absorbed the tree, telling Shisui he can't be defeated. Shisui picks up one of his kunai, powering up with his own Truth-Seeking Balls, that he would not be alone, as Sasuke appears beside him with a newly awakened Rinnegan as well. Madara notes he himself possesses both their powers and prepares to fight. Madara attacks, but Shisui and Sasuke evades it completely. Madara realizes they have discovered the working of his Limbo when Shisui and Sasuke ready their Jutsu. Madara escapes their simultaneous attack by sacrificing his Limbo and flies away to steal Kakashi's Sharingan. Sasuke manages to cut Madara in half, but he is a clone, then Shisui reaches his teammates and restores Kakashi's eye. Kakashi asks Sasuke what is his goal now, but before Sasuke can answer, he senses Madara's arrival and urges them to remember their teamwork. Madara arrives. Though scared, Sakura charges ahead, intent on creating an opening for Shisui and Sasuke, but is stopped by Madara's shadow. They retrieve her. Madara takes off to the sky, and creates multiple Chibaku Tensei, having them fall from the sky. Shisui and Sasuke move in to destroy them, while Naruto creates clones to deal with Madara's new shadows. In the sky, Madara recalls the text from the stone tablet, and removes the plating from his forehead, revealing a third eye. The eye opens and is reflected on the moon, casting the Infinite Tsukuyomi.

By reflecting his Rinne Sharingan on the moon, Madara activates the Infinite Tsukuyomi. The bright light traps every living being on the planet into the irresistible genjutsu. The only exception are Shisui, Sakura, Sasuke, Naruto, and Kakashi protected by Shisui's and Sasuke's Susano'o's, and the reincarnated Hokage. The trapped shinobi on the battlefield get caught in the roots of the God Tree one by one, despite interventions of Hiruzen.

Naruto tries leaving Sasuke's Susanoo, but Sasuke stops him, telling Naruto he'll also be caught in the Infinite Tsukuyomi. Minato sees Konoha under the Infinite Tsukuyomi, the other great shinobi villages also under it. Tobirama unsuccessfully tries to free some shinobi from the roots of the God Tree. Black Zetsu notices Sasuke's Susanoo blocking the moon's Light. Kakashi tries speaking up but is shut down by Sasuke. Naruto berates Sasuke. Shisui explains they're likely the only ones not caught by the Infinite Tsukuyomi. Sasuke explains that as long as the light of the Infinite Tsukuyomi is shining, it's pointless trying to do anything, as the light of the Infinite Tsukuyomi fades and Sasuke and Shisui dispels their protective Susano'o barriers. Madara returns back to the ground and chastises the survivors, explaining why he believes Hashirama's dreams were flawed, but before he can do much more, Black Zetsu suddenly stabs Madara through the heart.

Exclaiming in shock, Madara begins to swell and huge amounts of chakra are drawn to his location. Sasuke and Shisui attempt to stop the plan from succeeding, while Black Zetsu explains that he has been waiting for this moment for eons and that it is the will of Kaguya Ōtsutsuki. Madara asks why the tablet said the technique would calm all wars in the world, only to realize in shock that Black Zetsu had made revisions to the tablet and that he was merely a pawn for the revival. Just before he is swallowed, he dwells on his mistakes, before the swelling stops and Madara is replaced by the reborn Kaguya.