After the end of the Third Great Ninja War, the Leaf Village is divided over who should become the next Hokage.

Kakashi becomes part of the ANBU Black Ops, an elite team of shinobi who are under the direct command of the Fourth Hokage, Minato Namikaze.

At the Foundation, Kakashi meets a boy who uses Wood Style, a jutsu that only First Hokage Hashirama was capable of using. Kakashi goes to Third Hokage Hiruzen’s library to seek answers and discovers records regarding Hashirama’s cells.

Orochimaru is forced to flee the Hidden Leaf after Third Hokage Hiruzen exposes his illegal experiments. Danzo, fearing that Orochimaru’s capture would lead to the exposure of his own involvement in the experiments, sends out one of his men to help.

While pursuing Orochimaru, Kakashi wanders into a village inhabited by the Iburi Clan, a group of people with the unique ability to turn into smoke. Kakashi is soon captured and learns that the villagers all serve under Orochimaru.

Yukimi leaves the village to see the outside world, taking “Tenzo” with her. Kakashi tries to convince the two to return so that he can set a trap to capture Orochimaru, who is after Yukimi’s blood.

Danzo orders Tenzo to kill Kakashi and take his Sharingan. Reluctant at first, Tenzo decides to carry out his orders after learning that the Leaf Shinobi has come to be known as “Kakashi the Friend Killer.”

After being saved by the target he was ordered to kill, Tenzo realizes that the man known as “Kakashi the Friend Killer” is someone who values the lives of his comrades more than anyone.

Itachi Uchiha is inducted into Kakashi’s unit as the youngest member of the ANBU Black Ops. Itachi’s father, Fugaku, is pleased, thinking this will grant the Uchiha access to exclusive, top-secret Leaf intel.

Following the aftermath of the Nine-Tails incident, many on the Leaf Council voice suspicions that the Uchiha Clan were behind this tragedy. The Uchiha are then placed under 24-hour surveillance by the ANBU, which causes further tensions to arise.

Kakashi visits the Uchiha District and notices that the community seems more antisocial than the last time he visited. Meanwhile Itachi finds concrete evidence regarding the Uchiha Clan’s coup against the Leaf. The fateful moment is fast approaching…

Now relieved from his Anbu duties, Kakashi starts his day as jōnin and instructor to genin. He recalls his past mistakes on his training days with his former sensei Minato Namikaze and tries to make his own way in instructing his candidates. Hiruzen notices the "darkness" still embedded in Kakashi's heart. Meanwhile, Guy trains Lee, Neji and Tenten and the young shinobi successfully excel in their training. As they rest, they talk about Kakashi's way of training and this makes Guy worry. At the Dango Shop, Guy talks to Asuma and Kurenai about Kakashi and suddenly Hiruzen joins them. After Kakashi continuously ignores Guy, he is stormed by his former students and thanked him for the lessons he taught from the bell test. Hiruzen finally reveals the next genin team to be assigned to Kakashi: namely Sakura Haruno, Sasuke Uchiha, and Naruto Uzumaki.

Hiruzen informs Kakashi that he would be assigning him to another genin team and though Kakashi is hesitant at first, his interest is peaked when the Third mentions that Minato's son was to be assigned to his team. The two make unofficial visits to both Naruto, and the other two team members' homes. While visiting Sakura's, they encounter her parents Kizashi and Mebuki who invite them inside. Hiruzen would later explain his rationale behind formulating the teams, Kakashi ultimately accepts his new assigned team. Back at the Academy, Team 8 and Team 10 are assigned to Asuma Sarutobi, and Kurenai Yūhi respectively, leaving Team 7 alone at the Academy. Kakashi, who is at the Memorial Stone speaks briefly with Yamato who notes that his senpai was changing if even very little at a time.