Returning from the mission, Naruto recollects his strange encounter with Itachi. What did the now deceased Itachi wish to tell him? As Naruto ponders this, Kakashi makes an abrupt visit.
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 and his friends successfully decipher the code Jiraiya left behind with the help of some information Naruto has. The crew immediately calls Fukasaku over, but the message is not enough to solve the mystery of Pain.
At Mount Myoboku, Naruto begins his Sage Jutsu training under Fukasaku. The first challenge is "Don't move." Fukasaku explains that an extensive amount of time is necessary in order to take in nature energy.
Naruto continues his Sage training at Mount Myoboku, but with very slow progress. Fukasaku runs out of patience and suggests they move on to the next training…
Shikamaru and the others wait for the information Jiraiya brought back to be analyzed. The Hidden Leaf ninja continue their data analysis, when disaster strikes the village.
The Leaf Village is under heavy attack from Pain and Konan. Hearing the Akatsuki attack, Tsunade attempts to contact Fukasaku…
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.
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.
Tsunade comes face to face with Tendo Pain on the rooftop of the Hokage mansion. When Pain demands the Nine Tails be handed over, Tsunade refuses. However, Pain uses the Ningendo's power to learn of Naruto's current location in Mount Myoboku. Tsunade clenches at the sight of the growing number of casualties within the Leaf. But Pain, who condemns the Leaf's arrogance as a major nation, makes the choice to deliver catastrophic damage against the Leaf Village to teach them what true pain is.
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.
Naruto hits Pain with his Sage Jutsu-perfected Wind Style Rasen Shuriken. Although he succeeds in defeating Ningendo, the remaining Pain quickly confronts him.
Gamabunta and the other toads are defeated while Naruto is captured by Pain. Naruto attempts to fight back with Sage Jutsu, but Gakido sucks out his chakra, forcing him to go out of Sage Mode.
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 loses himself after seeing Hinata taken out right before his eyes. His anger triggers the Nine Tails' chakra to go out of control.
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.
To break the cycle of hate, Naruto heads to where the real Pain is hiding.
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."
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.
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 remains silent after learning of Nagato's painful past. Nagato claims true peace cannot exist in this cursed world, dismissing Jiraiya's ideal as nothing more than wishful thinking.
Nagato, having decided to believe in Naruto's word, performs his last forbidden jutsu: Gedo Art Rinne Rebirth.