Naruto and Kakashi continue to pursue Deidara while Sakura and Chiyo continue the battle with Sasori. Sakura manages to shatter Sasori's puppet body, but he reforms. Chiyo summons the Ten Puppets of Chikamatsu.. Sasori, remarking on Chiyo's ability to control so many puppets, summons one hundred human puppets and the final battle begins. Sakura and Chiyo seem to trap and defeat Sasori but, under cover of the battle, Sasori, who had transferred himself to another puppet, attacks Chiyo from behind. Sakura intercedes, taking the sword thrust meant for Chiyo.

Chiyo injects the last remaining antidote into Sakura and manages to stab Sasori in his only living part, his heart, using the Father and Mother puppets. With Sasori immobilized, Chiyo revives the nearly dead Sakura using her Resurrection Technique. As he dies, Sasori rewards Sakura for defeating him, telling her where he planned to meet with one of his spies who had been working undercover as one of Orochimaru's subordinates. Meanwhile as Kakashi and Naruto are pursuing Deidara, Kakashi reveals his plan to activate his version of Mangekyo Sharingan.

Team Guy's fight continues as they fight their respective clones. Neji explains to each member of the team that they are growing weaker and weaker as the fight drags on and they become fatigued. Their clones being non-human remain as strong as they were when they were formed. Lee, who refuses to accept defeat, realizes that the only way for them to defeat their clones is to become stronger than they were when they first started fighting. After a flashback about their training sessions, they all remember that they resolve to constantly become stronger. The memory gives them the strength needed to overpower and defeat their clones with new techniques that they devise.

After Team Guy members finish their battles, they make their way to Team Kakashi. Sakura and Chiyo also make their way towards Naruto and Kakashi. Kakashi reveals his Mangekyo Sharingan, which he uses to warp space around Deidara, hoping to suck him into an alternate dimension. However, he only succeeds in catching Deidara's arm, severing it. Kakashi's second attempt fails when Deidara dives into the trees. While Deidara has his guard down, Naruto manages to separate him from his clay bird, having his clones take the beak, which contains Gaara's body, to safety. Naruto, meanwhile, launches a vicious attack on Deidara, only to discover that he is beating up a clay replacement. In his angered state, Naruto's fox chakra begins to emerge. The two tailed form of the nine tailed fox emerges.

After Naruto is taken over by the nine-tailed fox's chakra, Kakashi uses the seal Jiraiya gave him to suppress it. Team Guy finds Deidara thanks to Neji's Byakugan. Deidara seemingly self-destructs while attempting to kill his attackers by creating a massive explosion after eating the remains of his chakra infused clay bird. The explosion is countered by Kakashi, who is able to send it to a different dimension. Sakura cannot bring Gaara back to life, and the group mourns Gaara's death. While the group mourns, Chiyo moves over to Gaara's body and uses the life-resurrection technique.

Chiyo finishes her life-resurrection technique with Naruto's help. As she is about to finish her technique, she passes down to Naruto and Sakura her wisdom for the future. A revived Gaara finds himself surrounded by shinobi from Sunagakure celebrating his return. After Gaara discovers that Chiyo has passed away, he asks everyone to pray silently for Chiyo's sacrifice.

Deidara survives his battle and begins to search for his missing arm. Meanwhile, Zetsu and Tobi, who wishes to join Akatsuki, search Sasori's remains for his ring. Deidara later finds the two searching for his own ring. The leaf ninja leave Sunagakure after their victory, and Danzo gives Sai instructions for his new team, Team Kakashi. The leaf and sand ninja pay their respects at Chiyo's grave, and Gaara and Naruto shake hands before departing.

Teams Kakashi and Gai return home to Konoha. As Kakashi rests in the infirmary, Sakura tells Tsunade about the information Sasori gave her as a reward for defeating him. Sasori had a meeting scheduled with a spy from within Orochimaru's ranks in 10 days. 4 days have passed since Sakura received this information, and now Naruto and Sakura need to recruit a new team member to go and investigate. As Naruto searches Konoha for a willing recruit, he meets some of his old friends. Just as Choji agrees to help, Shikamaru, Choji and Naruto are attacked by a Konoha shinobi unknown to them, Sai.

Naruto, Choji and Shikamaru attempt to capture and interrogate Sai, but Sai withdraws after insulting Naruto. Concerned that the Kyuubi could fall into Akatsuki hands, the village elders challenge Tsunade's plan to send Naruto out of the village without the still bedridden Kakashi. Tsunade promises to protect Konoha with her own life if Naruto is captured, but is still forced to compromise with Danzo by adding Sai to Team Kakashi. She also temporarily replaces Kakashi with ANBU member Yamato and warns him to keep an eye on Sai. Naruto and Sakura finally meet their new team members, and Naruto is immediately angered to see Sai is a part of the team.

Yamato takes temporary leadership of Team Kakashi while Sai insults both Naruto and Sakura. While preparing to set off, Sai receives an envelope from a Root shinobi containing secret orders from Danzo, and Sakura consults with Tsunade. Jiraiya then meets with Tsunade and Yamato in Kakashi's hospital room to brief Yamato on the demon fox within Naruto, detailing the "demon fox's cloak", and revealing a scar he got from Naruto when the fourth tail formed. Finally the new Team Kakashi set off on their new mission, to intercept an Akatsuki spy and gather information about Sasuke.

The new team Kakashi heads out for the Heaven and Earth bridge. Sai, Sakura, and Naruto come to blows after just 5 minutes on the same team due to Sai making fun of Sasuke. Therefore, Yamato decides they need to improve on teamwork and uses Mokuton to create a wooden cage threatening to lock the team up unless they behave. Given an ultimatum between being locked up or spending the night at a hot springs, the team chooses to visit the springs to improve team cohesion. Naruto still despises Sai despite this effort, and several insulting remarks from Sai worsen team relations.

Sakura sees Sai drawing by the river and finds out that Sai has artistic talent but has never given titles to anything he ever drew. Naruto and Sakura begin to realize the reason behind Sai's repulsive personality. After the hot springs, the team heads off to the bridge to meet the spy. Yamato is suspicious of traps so they go off the main road into the forest. Camping for the night, Yamato then creates a two story house by again using his Mokuton jutsu. Inside this house, the team formulate their plan.

Naruto is paired with Sai for the Buddy team of two, over his and Sakura's objections, while Sakura is assigned to support Yamato. Yamato conducts a simulation of the spy meeting with himself as the spy to gauge Naruto and Sai's abilities and teamwork. After Naruto makes a mistake when attacking Yamato, Sai immobilizes him and goes on to capture Yamato alone. Naruto is angry with Sai for not acting as a comrade would, but resolves to work together with him if doing so will help bring Sasuke back. Sai reveals to Sakura that he has no emotions, and little understanding of them. The group then prepares to head to the bridge.