Relying on Naruto's power, Granny Chiyo performs the Transmigration Jutsu on Gaara.

Yamato disguises himself as Sasori after creating a wood replica of Hiruko, and goes to meet the spy. The spy turns out to be Orochimaru's right-hand man, Kabuto Yakushi, who reveals the location of Orochimaru's current hideout to Yamato. Orochimaru interrupts the meeting, appearing to attack Kabuto, and while it initially appears that Orochimaru has come after Kabuto, Kabuto attacks Yamato and reveals that he is truly loyal to Orochimaru. Orochimaru calls out Naruto, Sakura and Sai from where they are hiding and observing the meeting, and prepares to fight the team.

Kabuto creates a fake corpse that resembles Sai, containing hidden traps to slow down Yamato's clone after sensing it. Naruto hasn't completely recovered from using the Demon Fox's chakra, and Yamato says that he will be left behind if he cannot keep up. Naruto is determined to finish his mission and not slow the team down. However Team Kakashi is forced to take a break when it's clear that Sakura has not fully recovered from her own injuries. Yamato then uses this opportunity to talk to Naruto alone and reveals to him that the one who hurt Sakura was Naruto himself. Naruto is shocked by what Yamato says to him.

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.

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 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.

Team Asuma continues their battle with Akatsuki's Hiden and Kakuzu.

Sasuke fights Killer Bee and is injured by his swords. Karin heals him, and Sasuke, Suigetsu, and Jugo then begin a combined assault on Bee until he decides to use the Eight-Tails' power. Sasuke is injured and revived again by Jugo, who regresses in age as a result. All healed, Sasuke unleashes Amaterasu on Bee, finally able to subdue him. Meanwhile, two Cloud ninja watch the fight from a cliff, and they notice the Uchiha crest on Sasuke. They rush the news to Bee's big brother, the Raikage.