Kakashi is released from the hospital and begins Naruto's training program. Naruto learns that he has Wind-style chakra. Yamato helps by setting up the training field with his special jutsu. Naruto also learns that he can use his Multi Shadow Clone jutsu to speed up his training, since whatever the clones learn, the original user learns upon the clone's dispersal. Naruto and his mass of clones each take a leaf and attempt to slice it in half with wind chakra as the first step to creating his new jutsu.

Naruto and his clones continue to work on chakra nature manipulation by slicing leaves. After some struggling, Naruto approaches Asuma, who is also a wind type, for advice, after which Asuma gives Naruto's clone a few pointers. Naruto is subsequently able to slice a leaf in half. Asuma and Yamato head out with their teams on new missions. It is revealed that Asuma is the Third Hokage's son and that he is in a relationship with Kurenai. Meanwhile, on a hill overlooking a burnt village, four cloaked figures discuss the awakening of the Fire Country by eliminating the Leaf Village.

Naruto's been having nightmares about the release of the Nine-Tail's power. Afterward, Kakashi informs Naruto that he has special training for him that will make him strong quickly. They are cut off by Team 10, who have also come to visit. Sai lunches with them and, trying to make friends by using nicknames, angers Sakura by calling Ino "gorgeous" after concluding that women do not like to hear how they really are.

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.

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.

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.

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.

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.

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.

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.

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.