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

The is the seventh filler arc from Part II of the series and spans from episode 349 onwards. The arc focuses on Kakashi Hatake's ANBU background, taking place after the battle at the Kannabi Bridge, losing his closest friend Obito Uchiha, and later taking Rin Nohara's life with his own hands. This arc takes place in the middle of the Ten-Tails Revival Arc.

Kakashi's Trauma
The previous Ino–Shika–Chō is sent out to complete an Iwagakure treaty mission. Iwagakure doesn't intend to keep a peaceful treaty, but as the meeting happened at the border with the Land of Wind, the Fourth Kazekage ensured no fights would break out near his country. The Iwagakure-nin return and update the Third Tsuchikage about the events. In Konohagakure, Kakashi still feels guilty about his role in Rin's death. In a meeting with the council, Hiruzen decides to step down in favour of a new Hokage. Danzō proposes Orochimaru, but Hiruzen suggests Minato over him. Minato takes over as Hokage, and when Kakashi continues to struggle with his trauma, Minato has Kakashi become an ANBU. Kakashi becomes as an ANBU, frequently killing opponents in cold blood. To mitigate this, on Hiruzen's suggestion, Minato has Kakashi do surveillance on Kushina, whose pregnancy as a jinchūriki becomes a matter of great importance, as well as hoping that a more cheerful mission will help him.

When the Nine-Tails attacks Konoha, Minato and Kushina contain it at the cost of their lives. Kushina lives just long enough to tell Hiruzen Naruto's name and plead to protect him. Hiruzen resumes his duties as Hokage, and Danzō invites Kakashi to be part of Root. Upon first reporting, he meets another Root agent, one who is capable of using Wood Release. Intrigued by it, Kakashi breaks into the Hokage's residence to search for secret files on those abilities, and is caught by Hiruzen, who shares with him the story of the village's early experiments to replicate them, and the disappearances that came with the experiments. Danzō plots to have Hiruzen assassinated, but Kakashi foils his plot. However, he allows the would-be assassin, the boy with Wood Release, to escape, certain that his ability will one day be valuable to Konoha. Kakashi tells Hiruzen about Kinoe's existence, and continues to be an ANBU under his command.

Orochimaru's Defection & The Iburi Clan's Downfall
When Orochimaru's illegal experiments are discovered, Hiruzen leads an ANBU team to apprehend him, but is incapable of killing his own student, allowing Orochimaru to escape. Kakashi tries to deter Orochimaru from leaving the country's borders, but is defeated. Orochimaru is injured by an exploding tag hidden inside a snake. Danzō sends Kinoe to aid Orochimaru leave the country, and when he reaches a meeting place, he encounters a clan who can turn to smoke, that is also loyal to Orochimaru. One to the clansmen, Yukimi, believes Kinoe to be her long-lost brother Tenzō. Kakashi arrives at the clan's hideout, and is attacked by another member, Gotta. Kinoe prevents Gotta from killing Kakashi under the pretence of interrogating him, and reveals to Kakashi that his true mission is to stop Orochimaru from leaving the country, as his great knowledge from his experiments would be detrimental to Konoha if he left the country. Gotta, who had been listening in, attacks both of them, but Yukimi helps them escape. Yukimi possesses Kinoe so she can experience the outside world without having to worry about the wind dispersing her in her smoke form, and Gotta begins fighting Kakashi again, before he himself is fatally dispersed as smoke. With his dying breath, he tells Kakashi that Orochimaru is after Yukimi. Kinoe refuses to sacrifice Yukimi when he learns this from Kakashi. Orochimaru reaches the Iburi clan's hideout and begins attacking them for their blood, desperate to acquire their ability. While Kakashi and Kinoe fight, Yukimi escapes and goes back to her clan's hideout to save them, but arrives only in time to see them dead by Orochimaru's hand. Kinoe and Kakashi reach them, but Orochimaru is able to capture Yukimi. The two are able to track Orochimaru down with the help of the deceased clansmen, whose smoke leads them where Orochimaru tries to acquire Yukimi's ability. The stress is to great on her, and she begins to turn to smoke, so Orochimaru escapes. Kinoe tries to contain Yukimi's smoke with his Wood Release, and is aided by the smoke of her deceased clansmen, managing to return her to human form, her ability stabilised. Yukimi departs, and Kakashi tells Kinoe that he won't report having found Orochimaru or the Iburi clan.