The Chunin Exams finally begin and the proctor for Round One is none other than Shikamaru!

The genin are unable to figure out the answer and start to panic.

On the night before the Second Exam, the entrants gather in the cafeteria, and a brawl breaks out.

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.

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.

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.

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.

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.

Team Kakashi returns to the Hidden Leaf Village after completing their mission. As Naruto thinks back to the talk he had with Itachi, he's summoned by Tsunade, where he discovers shocking news regarding Jiraiya.

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.

Yamato uses the first Hokage's chakra to suppress the demon fox's chakra and Naruto returns to normal, but with severe injuries. Sakura begins to heal him, but notes that medical ninjutsu has little effect on his wounds. Orochimaru's sword is revealed to have only pierced one of Sai's clones. The real Sai emerges, talks to Orochimaru and gives him a letter from Danzo. Sai then leaves with Orochimaru and Kabuto but Yamato's wood clone stays close on their trail. Naruto comes to his senses and wonders what happened but Sakura decides not to tell him the truth. They reach the meeting spot, picking up the picture book Sai left behind. Yamato infers that Danzo seeks to destroy and remake Konoha by collaborating with Orochimaru.

Yamato and the team enter Sai's room and confront him while Kabuto makes his way there as well. Sai tells Team Kakashi that not only was he to help with Konoha's destruction but also act as a spy against Orochimaru. Yamato reveals the secret of "Root"- its members were trained like Kirigakure's students in that they had to kill their friends so as to eliminate their emotions. Sakura returns Sai's book to him, remarking that he still has emotions because he treasures it. Sai then tells the group about his bond with his brother. Finally the team decides what to do about Sai's betrayal outside the lair. In doing so, Naruto tells the group about his own bonds and about how far he's willing to go to bring Sasuke back.

Kabuto fights Team Kakashi and frees Sai. However, Sai, who intends to learn more about his bond with his brother through Naruto's bond with Sasuke, betrays him. Captured, Kabuto gives a vague description of Sasuke's location to the team. Leaving Yamato's wood clone to watch over Kabuto, Team Kakashi enters Orochimaru's hideout and splits up to find Sasuke.

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.

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.

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.

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.

Kabuto comments that Naruto's state is a consequence of his desperation to bring back Sasuke. Sakura begins to cry and approaches Naruto but is injured when his attention turns to her. Yamato uses the mokuton jutsu to bind Naruto before he does any more harm. Kabuto heals Sakura, reasoning that the Konoha ninja are not Orochimaru's enemies because they are also fighting Akatsuki. Yamato uses the abilities of the 1st Hokage to forcibly return Naruto to his normal state. Meanwhile Sai confronts Orochimaru with a message from Danzo. Orochimaru responds by piercing Sai with Kusanagi.

Sai receives a chilling glare from Sasuke's Sharingan that frightens him. Sai gives Orochimaru a bundle with information about Konoha's ANBU. Yamato gives Sakura and Naruto seeds with his chakra that enables him to track them inside the lair, and reveals that he was able to track Sai because he put a seed in Sai's clothing and food during the visit to the hot springs. Kabuto locks Sai in a room, and the boy summons a bingo book from scrolls he carries. Yamato uses a jutsu to open a tunnel into Orochimaru's hideout, and he, Naruto and Sakura travel to Sai's room undetected.

Orochimaru and Kabuto convince Sasuke to withdraw with them, and Naruto weeps over his failure to return Sasuke to the village, but Sakura reassures him that they will bring Sasuke back together. Naruto's team reports to Tsunade about the results of the mission, and Tsunade is greatly angered over Danzo's scheme, particularly his leaking classified information to further it. Sai asks Danzo to allow him to remain with Team Kakashi, and Danzo reluctantly agrees. Sai goes on a mission with his team, having come to see them as his friends.