Naruto ha un incubo dove vede un individuo misterioso sprigionare la forza della Volpe a Nove Code. Dopo essersi ricordato del recente incontro con Sasuke, Naruto si rende conto che si è trattato solo di un brutto sogno. Nel frattempo, Sai inizia a studiare i vari metodi per socializzare con gli altri e a utilizzare i soprannomi, ma la cosa si presenta alquanto difficile per lui. Naruto, Sakura e Sai vanno a visitare il maestro Kakashi in ospedale e quest'ultimo avverte Naruto che, una volta dimesso, lo sottoporrà a uno speciale addestramento per creare una nuova tecnica più potente del Rasengan. Prima che Kakashi possa spiegare i dettagli a Naruto, arriva Asuma con il Team 10 al completo.

Kakashi viene dimesso dall'ospedale e inizia il programma di allenamento di Naruto. Naruto scopre di avere il chakra di tipo vento. Yamato lo aiuta preparando il campo di allenamento con il suo jutsu speciale. Naruto impara che può usare la sua tecnica superiore della moltiplicazione del corpo per accelerare il suo allenamento, poiché qualsiasi cosa i cloni imparano,viene trasmessa alll'originale quando il clone viene disperso. Naruto e la sua massa di cloni prendono ciascuno una foglia e tentano di tagliarla a metà con il chakra del vento come primo passo per creare il suo nuovo jutsu.

Naruto e i suoi cloni continuano a lavorare sulla manipolazione della natura del chakra, affettando le foglie. Dopo qualche difficoltà, Naruto si avvicina ad Asuma, che è a sua volta un tipo vento, per un consiglio. Naruto è quindi in grado di tagliare una foglia a metà. Asuma e Yamato escono con le loro squadre per nuove missioni. Viene rivelato che Asuma è il figlio del Terzo Hokage e che ha una relazione con Kurenai. Nel frattempo, su una collina che domina un villaggio bruciato, quattro figure nascoste discutono del risveglio del Paese del Fuoco attraverso l'eliminazione del Villaggio della Foglia.

Naruto, Sakura, Sai and Yamato head out for a new mission near the Fire Temple. When the other party fails to show up at the rendezvous point, the team gets separated and Naruto stumbles upon one of the four hidden tombs they came to protect. Due to a misunderstanding, he fights one of the monks-in-training from the Fire Temple, Sora, who also uses wind chakra based techniques. After the confusion, the monks and Team Kakashi travel to the Fire Temple, and Naruto recognizes it from his nightmare.

The temple monks explain that the tombs hold the loyal bodyguards of Fire Country's feudal lord. Naruto observes Sora sparring with other monks and becomes offended upon realizing he is holding back. Naruto challenges Sora, but just as the matter is about to get serious, another monk stops him. Naruto realizes Sora is despised by the other monks as he was himself and wishes to befriend him. Naruto visits Sora again and observes him practicing his wind jutsu in earnest, hoping to get strong enough to avenge his father. They later return to the temple to receive news that another tomb has been robbed.

Tsunade suspects that Danzou is plotting something and orders an investigation of him. Team Kakashi, Chiriku and Sora notice the coffins moving on their own, but fail to intercept them. The coffins emerge on a cliff, where the leader of the enemy ninja orders his subordinates to deal with their foes. The ninjas turn the area into a maze of rocky canyons and pits, full of deadly traps. The team members are separated from each other, and begin facing off against the enemy. Yamato speculates that the ninja may have orchestrated the theft in order to target someone on his team.

Team Kakashi begins facing off against the enemy shinobi. Yamato eludes his opponent, Fudo, by faking his death. Sora, unwilling to look for Naruto, goes off on his own. Back in Konoha, Danzo reveals that he is aware that he is being watched by Tsunade's ANBU. Naruto fights Fūka, whose kiss is fatal and shows her ability to use earth, fire, water and lightning jutsus. Sai manages to escape from his attacker, Fuen, and later saves Sakura from an enormous spider, becoming injured in the process. Sora then hits upon the enemy leader, Furido, and it is revealed that he was the group's target.

Furido taunts Sora until Sora unleashes his true powers, before informing Sora that he is planning to use the four corpses to save the Land of Fire. Naruto continues his fight with F?ka and learns that she can use all five elements. F?ka manages to kiss Naruto and begins draining his chakra. Realizing that Naruto is in trouble from extra-sensory perception, Sora rushes to rescue him. Sakura, Sai and Yamato arrive to help but are trapped by Fudo and Fuen. F?ka drains Naruto's chakra until she begins drawing on the Nine-tails's, which is too unnatural for her to successfully absorb. The enemy team retreats when Chiriku brings reinforcements.

Asuma's team returns from its mission. Team Kakashi returns to Konoha as well, with Sora replacing Sai on the team. Naruto tries to show Sora around Konoha but Sora goes his own way. Sora's insults precipitate a brawl with Kiba and Choji, with Naruto and Rock Lee joining in. Shikamaru and Asuma stop the fight. Later Asuma tells Sora he knew Sora's father, who is revealed as one of the Guardians involved in the coup attempt. He also shows Sora his chakra blade attack. Furido and the other body snatchers begin their attack on the Kohaku Clan.

Asuma supervises Naruto and Sora's wind chakra training, and notices that Sora, like Naruto, has very powerful chakra. Tsunade and Yamato learn from Chiriku that Sora was inadvertently responsible for an incident in which the Temple of Fire was destroyed. Later, Asuma gives Sora a claw made from the same materials as his chakra blades. It is revealed that Asuma killed Sora's father Kazuma, who had planned to kill the Hokage. Furido then approaches Sora, telling him that Asuma is responsible for his father's death and passing him two "king" pieces from a Shogi set for Asuma. Danzo mysteriously disappears. Naruto approaches a furious Sora in the training grounds, who easily throws a chakra-powered kunai through a tree and destroys the stone behind it.

Danzou is brought in for questioning after being caught meeting with a young Rain ninja. Sora confronts Asuma, and Asuma admits to having killed Kazuma. He attacks Asuma, his arm once again assuming a demonic form. Afterward, Naruto gets injured while shielding Sora from the attacks of an unknown individual, presumably from Root. Furido then approaches Sora, telling him to kill both Asuma and the Hokage to avenge his father. Later on, Naruto catches Sora going after Tsunade. Sora retreats as Shizune and a few other ninja arrive, but Naruto pursues him. At that moment, a mysterious lightning storm strikes, cutting off power to the entire village.

With Konoha in complete darkness, the village struggles to defend against the four attackers who have sealed the entire village behind a barrier. The entire village is in a state of emergency. Asuma, commanded by Tsunade to follow Sora and Naruto, finally catches up to them. Asuma realizes that the four invaders plan to annihilate the entire village using the lightning powers of the corpses that they stole. The revelation shocks Sora. As Asuma leaves to help hold off the attackers, he instructs Naruto to continue pursuing Sora.

Konoha's ninja fight off the revived zombie members of the Kohaku clan. The four Guardian Ninjas, Seito, Tōu, Nauma and Kitane, are also revived. Asuma realizes that they are planning to use Limelight, a jutsu in which the four create a lightning blast powerful enough to destroy Konoha. Asuma sends Sakura and Yamato after the other three while he remains behind to battle Kitane, but Fuen tackles Sakura and Fudo fights Yamato. Meanwhile, Naruto catches up to Sora, but Sora runs off in search of Furido. Naruto tries to pursue him, but is assailed by Fuuka. Soon after, Sora reaches Furido, who admits that he had planned to destroy Konoha.

Sora refuses to let Furido destroy the village despite his grudge against Asuma and the Hokage. He is beaten up by Furido, who claims that his father had a similar flaw. Asuma gets trapped by Kitane in a force field of lightning. Meanwhile, Yamato and Sakura kill their opponents, and Shikamaru heads to the battlefield with a plan to defeat the zombies. Just as he puts it into motion, however, Fuen's barrier falls and Fudo's revival technique ends, and the zombies turn to dust.

Naruto deduces that Fuuka's secret consists of switching bodies to use each corresponding element and that her hair preserves her youth and body. Naruto damages her hair and it takes a life of its own dispensing the body, but Naruto finally kills it with a Rasengan. Meanwhile, Asuma manages to break free of the electric barrier, catch up with Kitane and defeat him in a short fight. Realizing that Kitane is no more, and that his three other companions were killed, Furido causes the 3 other ninja guardians to disappear. But Furido has a back up plan, Sora.

Furido releases Sora's seal, and tells him the truth: Sora is a pseudo-Jinchuuriki. The chakra that had leaked from the Nine Tailed Fox when it attacked Konoha 15 and a half years ago was harvested and implanted into Sora. Just then, Asuma arrives at the scene with Naruto. Asuma recognizes Furido and it is revealed that he is Kazuma, Sora's father. Yamato, Sakura, Kiba, Lee, Ino, Choji and Shikamaru also turn up. Enraged, Sora wants to destroy everything, and turns into the Three-Tailed form of the Nine-tails. However, Yamato is unable to restrain him, because he does not have the First's necklace on him.

The chakra of the Nine-tails rages out of control within Sora, preventing Naruto and the others from subduing him. Asuma and Kazuma resume their old battle, while Kazuma justifies his actions with his duty as a pawn to the "King" of the Fire Country. Naruto is repeatedly knocked down in his attempts to restrain Sora, and the chakra seeps into him and transforms him as well. Yamato is unable to suppress the Nine-tails' chakra in both Jinchūriki, being prevented by an unknown outside force. Sora's fourth tail emerges, causing the Nine-tails's Cloak to envelop his body. He temporarily gains his own consciousness when he witnesses Naruto stab himself in the leg and successfully prevent the original Nine-tails' Cloak from emerging.

The struggle between Naruto and Sora continues. Asuma and Kazuma fight. Sai arrives, having snuck out of hospital, and binds Kazuma with an ink snake. Kazuma breaks out of Sai's jutsu and charges Asuma, but is killed. Naruto eventually reaches Sora, who manages to release the Nine Tails's chakra. Sora then leaves the village to travel the world. Asuma and Shikamaru play shogi and discuss who the king of Konoha is. Elsewhere, two Akatsuki members, Hidan and Kakuzu, appear chasing the Two Tails Jinchūriki.

With the exception of Naruto’s Team 7, which is protected by the Susano’o, all other shinobi have been swept into a dream world by the Infinite Tsukuyomi. Even the Hokage, Tsunade, has fallen into a dream state. She awakens to find herself in the Leaf Village, where she discovers Jiraiya's final book, entitled "Jiraiya Ninja Scrolls," and begins to read...

Tsunade continues to read Jiraiya’s novel. Chunin- and jonin-level ninja have gone missing, and the Fourth Hokage, Minato, orders a search mission with teams of genin led by Guy and Kurenai. Kakashi’s Team 7 is also dispatched, but the hero Naruto Uzumaki, despite being the Hokage’s son, has the misfortune of being labeled a loser.

Tsunade continues to read Jiraiya’s novel. Chunin- and jonin-level ninja have gone missing, and the Fourth Hokage, Minato, orders a search mission with teams of genin led by Guy and Kurenai. Kakashi’s Team 7 is also dispatched, but the hero Naruto Uzumaki, despite being the Hokage’s son, has the misfortune of being labeled a loser.

Team Jiraiya, Shikamaru, and his Leaf teammates are lured into a mysterious village during their battle. A couple children from the village get caught in the crossfire and fall into a cave-in. Yahiko’s team rushes to the rescue, but Shikamaru doesn’t budge. Meanwhile, Naruto and Neji’s teams rendezvous, but a mysterious voice addresses them out of nowhere!

The Masked Man shows Neji and Naruto images of past incidents that occurred in the Leaf Village. Meanwhile, Shikamaru and friends join up with Team Jiraiya to rescue the children. After fighting side by side with the Leaf, Yahiko and the others seem to have a change of heart.

The Masked Man is satisfied that the Hidden Leaf Genin chose the importance of life over their mission, but orders his team to continue their surveillance. Meanwhile, Naruto is frustrated at his inabilities, and recalls why his father Minato sealed the Nine Tails inside of him.

Sasuke and Sakura join up with the others, but the Puppet User appears and blocks their path back to the Hidden Leaf Village. Sasuke wants to bring down the puppets and rush back to report to the Fourth Hokage, but Shikamaru and the others insist on staying and rescuing the jonin.

Jiraiya weakens the seal on the Nine Tails in order to help Naruto learn how to control the Tailed Beast's power. Jiraiya recalls the words spoken to him years ago by the Great Lord Elder. He told Jiraiya that he would have a student, and that his guidance would decide whether the student would save the Ninja World or destroy it.

Naruto joins up with the rest of his comrades, and together they overcome the puppet attack. The masked man witnesses this and is convinced there is a future for the young shinobi. He promises to release the kidnapped jonin and begins to explain the truth, and the situation behind his motives.

Naruto’s strength is recognized by his fellow genin, except Sasuke. But while Naruto enjoys a close relationship with his father, Sasuke’s father, Fugaku, constantly compares Sasuke with his older brother Itachi and barely pays attention to him…

Sasuke takes his frustrations out on Naruto and the two begin to fight, this time with their respective new jutsu. Minato steps in just before it turns into a disaster. From this encounter, Sasuke realizes that he is nowhere equal to Naruto in strength and joins the Leaf Police Force, determined to beat him one day.

Three years have passed since Sasuke joined the Leaf Police Force, and he's now lieutenant. But his abusive Police Force has only increased anxiety within the village, and the Uchiha remain in poor regard. Now that his training with Jiraiya has ended, Naruto returns to Hidden Leaf Village and has an explosive encounter with Sasuke in the middle of town!

Sasuke leaves the village in order to obtain power from Orochimaru. Naruto and his friends learn that Sasuke is in danger and decide to go after him. To keep this a secret, only Naruto and Shikamaru set out on this mission, but on the way the duo are accosted by masked ANBU shinobi!

The Anbu who attack Naruto and Shikamaru are agents sent by Danzo, who had promised Orochimaru that he would deliver Sasuke safely to him. Luckily, Neji, Lee and Tenten rush to their aid in the nick of time! Meanwhile, Hiruko reveals the truth behind the incident involving Hizashi

Naruto reaches the tower Sasuke was heading for, thanks to Neji, Lee and Tenten deterring the agents from the Foundation. But it's too late—Sasuke's already made contact with Orochimaru! Naruto passionately tries to reason with Sasuke, but ultimately their powers collide!

Sasuke has left with Orochimaru, but Naruto is not about to give up. Determined to bring Sasuke back, he returns to the village with Shikamaru and the others. Meanwhile, Yahiko appears in the village, calling himself “Pain" and seeking revenge for the Hidden Leaf’s betrayal.

Seeing Hinata almost die triggers Naruto’s anger and he goes into Nine Tails State. Naruto's power is enormous, but Pain releases his jutsu to seal him away. Hatred consumes Naruto as he tries to break the seal. With Naruto unable to calmly control the Nine Tails’ power, the village steadily heads toward destruction.

Several months after Pain’s attack, Jiraiya arrives with intel regarding the Akatsuki, who are attacking shinobi villages and kidnapping their Kage and jonin. He also reveals that Sasuke is working with them. Naruto is determined to bring his friend and comrade Sasuke back, once and for all!

Naruto wants to bring Sasuke back to the village, but Sasuke burns with a desire to bring Naruto down. Why is Sasuke so confrontational, and how did his feelings toward Naruto develop? The truth rises to the surface during Sasuke’s relentless attack. Where will this battle lead? Find out in the conclusion of the “Jiraiya Ninja Scrolls.”