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.

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.

Shikamaru continues his fight with Hidan. Hidan manages to injure Shikamaru and curses him the same way he did Asuma, but when Shikamaru survives Hidan's attack, Hidan realizes something isn't quite right.

Naruto runs into unexpected difficulties as he trains with Gamakichi and Gamatatsu. While Kakashi's group searches for Guren and her gang, Yukimaru seems to develop interest in Naruto.

Yūkimaru summons the Three-Tailed and immobilizes it while Guren tries to capture it. It manages to break free and attack. Kakashi tells Naruto to investigate the lake, while they find Rinji and the others. Rinji and his men prepare an ambush, but Hinata, Sakura, and Sai arrive to avert it. Naruto summons Gamakichi and Gamatatsu and approach the Three-Tails, where they see Yūkimaru and learn of his allegiance to Guren. Trying to save Guren, Yūkimaru tries to suppress the Three-Tails once more, before managing to escape with her.

Guren tries to attack Naruto within the Three-Tails, but, in her weakened state, is unable to do so and passes out. Meanwhile, Kakashi tells Sakura and Ino to heal Yūkimaru while he, Shizune, Kiba, Sai, and Hinata search for Naruto. Naruto and Guren soon encounter a horde of mini Three-Tails that try to attack them, but they evade them and begin to argue about Yūkimaru. While Yūkimaru awakens, Naruto summons a bunch of Shadow Clones to look for a way out of the beast's stomach. Elsewhere, Kabuto gives Curse Marks to Rinji's men.

Naruto, Sai, and Yamato arrive to save Hotaru and Utakata from the attacking ninja who they discover are Anbu from the Hidden Mist Village. Yamato attempts to negotiate alone with the head of the Mist Anbu, Tsurugi, and after their discussion, Tsurugi talks to Utakata alone. Tsurugi attempts to convince Utakata to return to the Hidden Mist Village but the latter refuses and remembers the horrible pain he suffered at the hands of his former master.

The reborn Team Kakashi continues to investigate the recent attack by Kabuto and the reincarnated shinobi when Naruto gets swallowed by a giant snake, but manages to escape using shadow clones, and accidentally ingests snakes that were present in the pond which Kabuto uses to summon Hidan.