After discovering a kunai knife with a secret message on it, Naruto winds up being pursued by three kunoichi from the Hidden Waterfall Village. Iruka mangaes to find him, but when the situation grows worse, Kakashi appears to save them both.

During the two-and-a-half-year time period in which Naruto was training under Jiraiya, the latter decided that it was time for Naruto to learn how to repel genjutsu. During this training session, the two traveled to a village which Jiraiya had previously been associated with, but they discovered that something dark was amidst.

Naruto thinks back to the time when he encountered the soul of a man named Kisuke. Kisuke didn't recall anything about who he was, but a visit to the Leaf Village's hospital revealed something startling. Meanwhile, higher-ups of the Fire Country met to decide on a new security system for the Leaf Village put together by a ninja named Sabiru. Who exactly were Kisuke and Sabiru, and what connection did the two have?

Naruto and Sakura learn that Danzo has been made Hokage and that his first order is to eliminate Sasuke. The two go to Sai and inquire about Danzo, but Sai reveals that a curse mark given to all members of the Foundation prevent him from revealing anything about the new Hokage. Soon afterward, Karui and Darui attack them, demanding information about Sasuke.

Naruto returns to the Leaf Village, and his teammates demand to know why he didn't finish Sasuke off when the latter was in such a weak state. Naruto tells them that when the time is right, he will deal with Sasuke personally. Meanwhile, a supposedly deceased member of Akastuki has infiltrated the Hidden Cloud Village.

Naruto gathers his friends and tells them that he will defeat Sasuke alone. Meanwhile, the Elders of the Leaf officially nominate Kakashi to become the next Hokage.

Konohamaru is eager to fight alongside his senior ninja in the coming war, but his young age prevents him from being assigned to the battlefield.

Inside his mind, Naruto continues his battle against Nine Tails to take control of its immense power.

Part Three of the Four Week Long Special Project for the Broadcast's Tenth Anniversary - Sasuke’s defeat to Gaara, and later Itachi, forces him to realize that he is not strong enough to get revenge against his older brother.

Taking place in the aftermath of the Kage Summit, Team Kakashi is sent out on a mission by Tsunade to a location known as "The Hole" to investigate an incident where its people were killed.