During the Chunin Exam, Neji rests in the medical room, having lost to Naruto. Just as Tenten comes in to check up on him, they see the Leaf Village attacked by Orochimaru and his men.

A beautiful kunoichi spy named Hanare is captured for attempting to gather intel on the Hidden Leaf.

Naruto is assigned to a team led by jonin Hayama to patrol the north border of the Leaf Village. One of his teammates is Kosuke, an old man who has been a genin for over fifty years, earning him the title "Eternal Genin."

Granny Cat requests that Sasuke and Team 7 collect the last cat paw print necessary to complete the "Paw Encyclopedia."

Naruto and Jiraiya attempt to save a village from Kandachi, a former right-hand man to Hanzo of the Hidden Rain.

Jiraiya takes Naruto to a village in the hopes of teaching him how to counter the Sharingan's genjutsu attack.

After accidentally finishing off Lee's last special youth drink, Naruto asks Guy to make more, only to learn one of its key ingredients, the Jofuku Flower, is out of stock. Naruto is determined to get the Jofuku Flower for Lee's sake.

Condor, the ostrich previously captured by Team 7, now lives in a forest with baby ostriches. Since his last escape, Condor has trained himself to become a ninja ostrich.

Tenten and Neji head for the Leaf Ninja Tool Research Lab to procure ninja tools necessary for rebuilding the Leaf Village.

Naruto visits Sakura, who is caring for Tsunade. Sakura recalls an incident that took place three years before, in which she collapsed from symptoms that resembled a disease caused by a mysterious virus.

Gaara, recalling a past mission carried out with the Leaf's Team 7, points out that the Leaf Village has Naruto with them.

Team 7 stops in a town for some rest, where they encounter a man named Tsukado who is out to avenge the death of his relative.

The Leaf ninja work to rebuild the Hidden Leaf Village. While helping with the restoration, Naruto and Sakura are reunited with two old friends—the carpenter Tazuna and his grandson Inari from the Land of Waves.

An emergency council is held before the Feudal Lord of the Land of Fire. The topic is to discuss plans to rebuild the Leaf Village, and Danzo strongly urges the council to select a new Hokage to replace Tsunade.

Naruto takes up his classmates' dare to venture into the forest and retrieve an item from the dead enemy ninja, unaware that the forest is still dangerous.

Naruto spends his days competing with Sasuke, the academy's star student, only to screw up and be the laughingstock of the class. Due to the childhood trauma of losing his parents to the Nine-Tailed Fox, Iruka finds it difficult to interact with Naruto as his student.

The Leaf Village is left in ruins in the wake of Pain's assault on the village. While cleaning through the remains of Ninja Academy, Iruka finds an old pillar and recognizes it as a memoir from Naruto's early years at the academy.

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

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.

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 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.

During a day off, Team 7 enjoys a barbecue on the beach. Naruto discovers a mysterious bottle and, upon opening it, releases a genie who claims to grant three wishes. Initially skeptical, the team soon realizes the genie's powers are real. However, their differing desires lead to chaos as they vie for the final wish. The story unfolds with comedic and action-packed sequences, showcasing the dynamics and personalities of the beloved characters.

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.

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.

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

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.

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.

Naruto hits Pain with his Sage Jutsu-perfected Wind Style Rasen Shuriken. Although he succeeds in defeating Ningendo, the remaining Pain quickly confronts him.

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.

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.

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.

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.

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 Pain and Konan. Hearing the Akatsuki attack, Tsunade attempts to contact Fukasaku…

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.

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…

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 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.

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?

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.

Hotaru, under the control of Shiranami's jutsu, uses the Forbidden Jutsu against Naruto and Utakata. Shiranami trembles with joy, having witnessed the power of the Forbidden Jutsu, while Hotaru is consumed by deep despair.

Naruto and Utakata successfully enter the Tsuchigumo village thanks to help from Sakura, Sai, and Yamato. Utakata senses the chakra filling the atmosphere and terrain behaving oddly, and together with Naruto, they enter the cave where the anomaly is originating.

Believing Shiranami's story, Hotaru writes a parting letter addressed to Utakata and leaves Mount Katsuragi. Meanwhile Naruto, still searching for Shiranami, falls into the Magaki Troops' trap but manages to escape thanks to help from Utakata.

Hotaru is brought back to the fort in Mount Katsuragi. Naruto, outraged to learn the forbidden jutsu was embedded inside Hotaru, demands an explanation from Tonbei. But it was none other than Hotaru herself who wished for this.

Yamato and Sai recognize their opponents as trackers from the Hidden Mist Village, but Naruto attacks without questioning. The Hidden Mist demands Utakata be handed over to them in exchange for Hotaru.

Having arrived at the village, Hotaru parts with Naruto and his team. But the Magaki Troops are one step ahead and threaten Hotaru to hand over the forbidden jutsu. Utakata appears, and Shiranami recognizes him as a bounty listed in the Hidden Mist's bingo book...

Naruto and his teammates are assigned to escort Hotaru, En no Gyoja's granddaughter, to the Tsuchigumo Clan's village located in the mountains. But Hotaru's mind is still attached to Utakata, who left after Naruto's arrival…

The Leaf ninja fail to capture Itachi and also lose track of Sasuke. Calling off their pursuit, the team is heading back to the village when an urgent assignment from Lady Tsunade comes in. The mission stems from a treaty between the Third Hokage and the En no Gyoja of the Tsuchigumo Clan...

The Taka split up with the Akatsuki to hunt down the remaining Tailed Beast. At the Land of Lightning they go up against Killer Bee, whose attack utilizing Lightning Style and seven blades proves to be more than a match for them.

Flame from the Amaterasu still remains on the battlefield as Naruto and his teammates continue to search for Sasuke. But despite the search team's best efforts, they cannot find any trace of him.