Naruto Uzumaki returns to Konoha after a two-and-a-half-year training journey with Jiraiya. He is reintroduced to his peers, who have advanced to Chunin rank or beyond, unlike Naruto who is still a Genin. Elsewhere, two members of Akatsuki head towards Sunagakure to capture Gaara, who has since become the Kazekage, the village leader.

Jiraiya tells Kakashi Hatake that Akatsuki's plan to collect the tailed beasts is underway. Because of the Demon Fox inside him, Naruto is in danger any time he leaves the village, so Jiraiya relinquishes Naruto's training to Kakashi, who can ensure his safety. Kakashi gives Naruto and Sakura a test to see how far they have improved. Meanwhile, the Akatsuki members Deidara and Sasori arrive at the entrance of the Sunagakure. They discover that Yura, their sleeper agent, has already cleared the guards.

Kakashi challenges Naruto and Sakura with the bell test, in which they must forcefully take from Kakashi two jingle bells using whatever means necessary. Sakura and Naruto both demonstrate their newly acquired skills. At Sunagakure, Deidara reveals his ability to manipulate exploding clay. He takes to the skies aboard a giant clay bird and begins his aerial assault by lobbing exploding clay spiders onto the guards, instantly killing them. As soon as he makes it to the Kazekage building, however, he finds Gaara there waiting for him.

Naruto and Sakura both realize that even though they have vastly improved, they are still no match for Kakashi's superior techniques, as he too has become stronger, and decide to resort to more unconventional means. They win the challenge by threatening to spoil the ending of Kakashi's new novel, forcing him to cover his ears and shut his eyes because of the Sharingan's ability to read lips. Meanwhile, Deidara and Gaara begin their battle. Deidara finds a formidable challenge in Gaara's abilities to control and manipulate sand.

Deidara sees that subduing the Kazekage is not as easy as he thought. He hurls exploding clay at Gaara to no effect, as Gaara can quickly summon a shield of sand around him with relative ease. Gaara then commands his sand to attack Deidara who has no choice but to try to evade. Gaara's sand eventually catches up with Deidara and crushes his arm.

Deidara is determined to capture the Kazekage. Unfazed by the loss of his arm, he unleashes a massive clay bomb onto the village. Gaara is able to deflect the bomb by using his sand to create an enormous shield over the village. However, this leaves him open to a sudden attack, and he inadvertently uses sand that had been seeded with Deidara's clay to defend himself. Deidara then detonates the clay-infested sand, which knocks Gaara unconscious. Deidara captures him and flies away.

As Deidara carries an unconscious Gaara out of the village, Gaara's older brother Kankuro chases after them. At the village entrance he discovers that all the guards there have already been killed. Upon catching Deidara and Sasori, Kankuro initiates his Puppet Technique by summoning his puppets Karasu, Kuroari, and Sanshouo. Sasori sees this as an opportunity to demonstrate his skills, and he allows Deidara to go ahead so that he can battle Kankuro alone.

Kankuro's attacks are all nullified by Sasori's scorpion-like tail. He eventually pierces Kankuro with his tail, inflicting him with a slow-acting poison. Kankuro is puzzled at how easily Sasori counters his fighting style. Sasori reveals that he himself used to be from Sunagakure and that Kankuro's puppets are his own creations. In response to the Akatsuki assault, Sunagakure sends a distress call to Konoha.

Kankuro is brought back to the village but he is feeling the effects of Sasori's deadly poison. The village's medics are helpless finding a cure. Baki decides to seek help from the village's elders, Chiyo and Ebizo. Meanwhile, Konoha receives the emergency message from Sunagakure. Tsunade chooses to send Kakashi, Naruto and Sakura to respond to the Sand's need. Along the way, Sakura learns for the first time that Naruto's body contains the demon fox.

Deidara and Sasori arrive at the secret Akatsuki hideout. The Akatsuki leader gathers his followers using an astral projection technique and they begin the ritual to extract the One-Tailed Shukaku from Gaara. At Sunagakure, Kankuro's condition is worsening and Chiyo claims that even her expertise is not enough to counteract Sasori's poison. At Konoha, Tsunade foresees the difficulty of Team Kakashi's mission and orders Team Guy to back them up.

After traveling for three days, Team Kakashi arrives just in time to save Kankuro. Using the skills she acquired from her apprenticeship under Tsunade, Sakura is able to extract the poison and create an antidote. Kankuro regains consciousness and gives Kakashi a piece of cloth from Sasori's outfit, allowing Kakashi's ninja dogs to track the Akatsuki member.

Team Kakashi heads out to Akatsuki's hideout along with Chiyo. On the way, Chiyo tells them about the Tailed Beasts. Meanwhile Pakkun heads out to Team Guy and informs them that they are quite close to the Akatsuki hideout. The Akatsuki send out Kisame and Itachi to stop Team Guy and Team Kakashi respectively.

The battle between Team Guy and Kisame begins while Kakashi explains the danger of Itachi's Mangekyo Sharingan to the rest of his team and reveals what he's discovered to be its weakness. Guy's team is quickly contained, leaving Guy himself to fight Kisame alone. Kakashi leads the attack against Itachi with Naruto following close behind, but Naruto is shocked when the real Itachi explodes into a cloud and his allies morph into Itachi clones.

The battle between Guy and Kisame gets into full swing. Guy bring outs his nunchaku to compensate for Kisame's sword, but takes a beating from Kisame's water attacks. Guy has to resort to opening six of the eight chakra gates to even the score. Meanwhile, Naruto realizes he is caught in an illusion and recalls his training with Jiraiya to try to dispel Itachi's illusion.

The two battles continue from the previous episode. Naruto is released from Itachi's genjutsu by Chiyo and Sakura after his failed attempt to release himself. Distracted and immobilized by Kakashi's shadow clone, Itachi takes a direct hit from Naruto's Great Ball Rasengan. Meanwhile, Guy defeats Kisame using his Morning Peacock technique. The Konoha shinobi then find, to their surprise, that they have not defeated Itachi or Kisame, but two entirely different people.

Kakashi's and Guy's teams both figure out that their battles with the doppelgängers were set-up to delay them from coming to Gaara's rescue. Chiyo reveals that in attempts to control the power of the tailed beasts they were bound to human hosts called "Jinchuriki", and that the human host dies when the beast is extracted — increasing the urgency of saving Gaara. Kankuro is awake and joins a meeting of the Sand council where the history of the Sand village is explained. Both teams stop to rest since their battles have taken their tolls and in preparation for the battles to come. Akatsuki sends Zetsu to dispose of the doppelgängers corpses.

Team Guy and Team Kakashi both finish their breaks and go on towards the Akatsuki lair. Naruto shows intense passion and is in a hurry to reach Gaara. Chiyo notices this and Kakashi explains to her that Naruto is also a Jinchuriki and knows the pain Gaara has lived through. Chiyo explains that she was the ninja who sealed Shukaku in Gaara, in order to protect the Sand village. Meanwhile, Akatsuki has finished extracting Shukaku from Gaara, who dies wondering if he has become a person whom others need. Team Guy and Team Kakashi finally meet in front of the sealed entrance to the Akatsuki lair.

Team Guy and Team Kakashi find out there is a barrier protecting the Akatsuki hideout, being generated by 5 forbidden tags in the area. After preparations, Team Guy removes the tags and disables the barrier allowing Team Kakashi to enter the hideout. Meanwhile the Akatsuki members have ended the astral projection technique and left the hideout. Deidara and Sasori who were the only ones physically present, remain behind to take care of the intruders.

Team Guy fights with exact clones of themselves, a trap set off by their removal of the barrier tags. Deidara takes Gaara's body outside of the cavern, followed by Naruto and Kakashi. Chiyo and Sakura stay behind to fight Sasori.

Chiyo explains to Sakura that Sasori used to be one of the best puppeteers in Sunagakure, but he began experimenting with real people. Sakura learns that Sasori's true body is hiding within his favorite puppet, Hiruko, ensuring that he cannot be attacked while controlling it. The only way to defeat Sasori is to destroy his puppet. Using teamwork, Chiyo and Sakura are able to dodge Sasori's attacks and demolish the puppet, from which Sasori himself emerges. Just outside, Deidara begins telling Naruto and Kakashi how much stronger Sasori is compared to himself.

With his puppet destroyed, Sasori reveals himself to Chiyo and Sakura, looking no older than when he left his village twenty years ago. As a further bit of nostalgia, he produces a summoning scroll and calls forth the Third Kazekage, whom Sasori has made into a puppet. Using its weapons, which are even more dangerous than Hiruko's, Sasori is able to catch Sakura in a poison gas cloud. Meanwhile, Kankuro, Temari's team, and Ebizo make their way towards the Akatsuki hideout.

Sakura manages to escape the poison gas cloud by using an explosive scroll on herself. Chiyo calls forth the "Mother" and "Father" puppets that Sasori created to fight him and the Third. They manage to hold down the Third for awhile until Sasori releases the Third's secret technique: Iron Sand. Meanwhile, Team Guy are having trouble fighting the clones and showing exhaustion from the battle. Naruto and Kakashi manage to avoid Deidara's clay bombs and keep up with him.

The Iron Sand stops both puppets from moving. Chiyo's right arm, which she had turned into a puppet arm, gets clogged as well. Chiyo thinks back to the past and remembers how Sasori created and controlled his first puppets, Father and Mother. Sakura urges Chiyo to use her again as a puppet. With Chiyo's help, Sakura avoids the columns formed by the Iron Sand to attack her.

Sakura and Chiyo continue their battle with Sasori, while Naruto and Kakashi follow Deidara, and Team Guy fights their clones. Sakura remembers her training with Tsunade when she was taught to observe enemies' weaknesses and dodge their attacks. Sasori attacks with an Iron Sand pyramid and prism, but Sakura is able to fend them off, causing a cave in. Sasori then uses a new technique to attack with randomly-growing iron spikes, landing a hit imbued with a poison that quickly paralyzes its victims. With a final attack of the Third Kazekage's puppet, Sasori attempts to kill the seemingly helpless Sakura, only to discover at the last second that it was a ruse. Somehow immune to the effects of the poison, Sakura destroys his puppet with a single punch at the last second.

Sakura reveals that she took an antidote against Sasori's poison which will make her immune to it for three minutes, forcing herself and Chiyo to end the battle quickly. Meanwhile, Naruto and Kakashi continue their pursuit of Deidara. Deidara attempts to split up Naruto and Kakashi by creating a swarm of explosive jumping crickets out of his clay and has them pursue Kakashi. Kakashi makes a shadow clone as a decoy and the crickets, mistaking the shadow clone for the real Kakashi, detonate harmlessly. Kakashi then catches back up with Naruto and reveals a plan. Sakura and Chiyo ready themselves for the battle with Sasori, who reveals that he made himself into a human puppet.