Kakashi's Anbu Arc: The Shinobi That Lives in the Darkness

Covering episodes 349 to 361, this arc is an anime-only production of Naruto: Shippūden inserted into the middle of the Fourth Shinobi World War's climax. It looks back on Kakashi's service in the Anbu Black Ops, using his story to also illuminate the pasts of Yamato and Itachi Uchiha. The events unfold across roughly a decade, from Minato's rise as Hokage to the night the Uchiha clan fell.

Haunted by his part in Rin's death, Kakashi is placed in the Anbu by Minato, where he kills without hesitation until gentler surveillance duty over the pregnant Kushina is arranged to steady him. After Minato and Kushina die containing the Nine-Tails, Danzō recruits Kakashi into Root, where he first encounters a boy wielding Wood Release. Intrigued, Kakashi digs into the village's buried experiments, foils a plot against Hiruzen, and spares the Wood Release boy, sensing his worth to Konoha.

When Orochimaru's crimes surface, Hiruzen cannot bring himself to kill his student and lets him flee. Danzō sends the boy, Kinoe, to aid the escape, drawing both him and Kakashi into the doomed Iburi clan, a people able to turn to smoke whom Orochimaru slaughters for their ability. Kinoe and Kakashi save the survivor Yukimi and grow to trust one another, and later, ordered to steal Kakashi's Sharingan, Kinoe instead protects him and takes the codename Tenzō after joining Hiruzen's Anbu.

Years on, a young Itachi enters the Anbu while Danzō assigns him to watch his own clan. As tensions boil toward a coup, Danzō steals Shisui's eye, driving Shisui to suicide and awakening Itachi's Mangekyō Sharingan. Itachi ultimately annihilates the Uchiha, sparing only Sasuke and securing Hiruzen's promise to shield him.

With the massacre behind him, Kakashi is discharged from the Anbu and told he will mentor a genin squad. Scarred by his own team's losses, he repeatedly fails candidates who neglect teamwork, until one trio catches his attention: his sensei's orphaned son, Itachi's younger brother, and a sharp kunoichi. When they grasp that helping a comrade outweighs the rules, Kakashi passes them and formally becomes the leader of Team 7, closing the loop on his darkest years.