Naruto comes face to face with Nagato and Konan. Naruto, wanting to confront the problem of their hate-filled ninja world, asks to hear Nagato’s side of the story before coming up with an answer.

To fulfill their dream, Nagato, Yahiko, and Konan walk through the war zone in search of Jiraiya, hoping to learn ninjutsu from him. After completing their training, the three form an organization with Yahiko as its leader.

Naruto and the others take on the oncoming challenges in order to find the secret technique and break the previous record set by the Fourth Hokage. But Naruto’s impulsive action leads the group into various troubles.

The story goes back to right before the start of the final rounds of the Chunin Exam. As Naruto trains in preparation for his upcoming match, he hears Jiraiya speak of “the Fourth Hokage’s legacy.”

To break the cycle of hate, Naruto heads to where the real Pain is hiding.

In one area of the village, Kakashi enters battle against Tendo Pain, but he can’t keep up with Tendo’s mysterious attacks. Shurado joins the fight, and Kakashi struggles with the two-on-one disadvantage.

Fukasaku and Shima fall in battle, leaving Naruto open to be captured by Tendo Pain. Just when all is thought to be lost, Hinata, who was following the battle with her Byakugan, steps in to face Pain.

Naruto wanders the streets of the Leaf Village, grief stricken over the death of Jiraiya. Unable to overcome his feeling of loss, Naruto traces back through his memories of Jiraiya. What can help the heartbroken Naruto get back on his feet?

Naruto loses himself after seeing Hinata taken out right before his eyes. His anger triggers the Nine Tails’ chakra to go out of control.

Nagato, having decided to believe in Naruto’s word, performs his last forbidden jutsu: Gedo Art Rinne Rebirth.

Naruto meets Minato Namikaze, the Fourth Hokage, inside his inner world. Before his death, Minato planted a fail-safe where he would appear within Naruto’s psyche should his son sprout eight tails.

Sensing danger at hand, Naruto, along with Fukasaku, rushes back to the Leaf Village from Mount Myoboku. But what they see is the remains of the Leaf Village, leveled beyond recognition.

In one area of the village, Kakashi enters battle against Tendo Pain, but he can’t keep up with Tendo’s mysterious attacks. Shurado joins the fight, and Kakashi struggles with the two-on-one disadvantage.

The Leaf Village is under heavy attack from the Akatsuki. Underneath the village Danzo takes action to achieve his ambition. Meanwhile, searching through the Rain ninja’s mind, Inoichi Yamanaka is about to stumble upon valuable information.

Nagato, having decided to believe in Naruto’s word, performs his last forbidden jutsu: Gedo Art Rinne Rebirth.

Konohamaru, Moegi, and Udon are shocked to see the disaster that has struck their home village. But to fulfill their duties as genin, each races out to direct the villagers to a safe location.