Team 7 continues to wait for the light of the Infinite Tsukuyomi to subside. Sasuke continues to ponder about Itachi's memories. In them, Fugaku congratulates Itachi on becoming an Anbu, but reminds him that his loyalty is first and foremost to the clan. Shisui entrusts Itachi with his remaining eye, and commits suicide, awakening Itachi's Mangekyō Sharingan. Itachi beats up Inabi, Yashiro, and Tekka, when they accuse him of having killed Shisui. Fugaku interrupts Itachi and questions what is happening, all while Sasuke is watching. Itachi proclaims that there is no hope for the Uchiha. Sasuke pleads with Itachi, asking him to stop. Itachi feigns regret, looking at Sasuke with his Mangekyō Sharingan, hoping Sasuke will realise how shallow the clan is. Itachi is later promoted to Anbu captain, and though not in Root, was to report to Danzō, who introduces Itachi to two subordinates under him and tasks them with an assassination. Upon returning from his mission, Danzō asks Itachi his opinion on the Uchiha, and Itachi shares their growing resentment of the village can no longer be ignored.
Fugaku orders Itachi to meet him alone after a clan meeting. Fugaku shows Itachi the Stone Tablet in the Naka Shrine, telling him his Mangekyō Sharingan should be able to decipher more of it than the Sharingan. Itachi asks if Fugaku wants him to read it for him. Fugaku reveals his own Mangekyō Sharingan, having awakened it during the Third Shinobi World War, when a comrade sacrificed himself to save him. Fugaku and Itachi discuss the clan's situation and wishes, which include Fugaku becoming Hokage. Fugaku has kept his Mangekyō Sharingan a secret from others, certain that if the Uchiha knew he could control the Nine-Tails, the conflict would escalate, and through genjutsu, shows Itachi what would happen. Fugaku wants to use Itachi's position as an Anbu to restrain the upper echelons of the village, so a coup can be bloodless. Itachi informs the higher-ups about the eminent coup. Despite Hiruzen's wish for diplomacy, Danzō gives Itachi an ultimatum regarding the assassination of the Uchiha. Itachi approaches Tobi for help. Tobi attacks the Uchiha at the police force, while Itachi attacks the ones at the compound. Izumi tries to attack Tobi, but in vain. Itachi shows Fugaku his own vision of the future, who releases his shadow clone. Itachi anticipates a fight with Fugaku, but he and Mikoto just wait for him, exchange final words before Itachi tearfully kills them. Itachi makes his final report to Hiruzen, before going in to join Akatsuki. On his way, he kills his previous Anbu subordinates when they try to kill him. In Akatsuki, Itachi is partnered with Jūzō Biwa.