After his failed attempt to retrieve Sasuke, Naruto learns that circumstances have granted him slightly less than three years to prepare for a confrontation with Orochimaru, who has to wait that much time before he can transfer into Sasuke's body. Naruto also must prepare for his eventual confrontation with Akatsuki, who are after the nine-tailed demon fox sealed within him. To prepare, Naruto leaves the village and undergoes intensive training under Jiraiya. At the same time, Sakura becomes Tsunade's apprentice, and Sasuke trains under Orochimaru. Thus, all three members of the original Team 7 are now training under one of the Legendary Sannin.
When Naruto returns to the village two and a half years later, he is reacquainted with his friends, who have all been training and growing as he has. When Naruto first got back to Konoha he found something changed as he looked at the mountain and saw Tsunade's face next to the 4th Hokage's. Where Naruto was once the shortest among his friends, he is now taller than most of them. He also finds out, much to his dismay, that he is the only one who has not progressed in rank over the timeskip. Most of his comrades have since become Chunin, and a few have become Jonin. Gaara even became the Fifth Kazekage after the death of his father, the Fourth Kazekage. After the reintroduction, Jiraiya leaves Naruto with Kakashi Hatake. Team 7 is reformed as a three-man squad with Naruto and Sakura and they commemorate this by having another bell test. Unlike the first bell test, the point of this one is to actually get the bells. Using their new skills and Kakashi's obsession with the Icha Icha novels, Naruto and Sakura take the bells from Kakashi.
Naruto is given little time to reminisce, however. In Sunagakure, the Akatsuki team of Deidara and Sasori attempt to kidnap Gaara. Despite his improved ability, Gaara's newfound desire to defend Sunagakure proves to be his downfall when Deidara threatens to destroy the village with his Explosive Clay. Kankuro then attempts to stop the Akatsuki members, but his puppets are easily fought off and destroyed by Sasori - revealed to be the maker of Kankuro's puppets. Sasori also poisons Kankuro in the process, leaving him to die within the next three days. The Akatsuki duo take Gaara back to their lair, where their leader summons a massive statue to extract and seal in Gaara's demon. The sealing ritual takes three days.
Upon hearing of Gaara's kidnapping, Team 7 leaves for Sunagakure with Temari, who is in Konoha to help with the most recent Chunin Exam, as she is now a Jonin, and a liaison from Suna. On the way, Naruto tells Sakura and Temari that he is the host of the nine-tailed demon fox and that Akatsuki is after the demon inside Gaara. This gives Sakura some insight into what Naruto has gone through. After learning this information, she vows to do everything she can to protect Naruto from being a victim of Akatsuki. Temari is thankful that there is someone who can understand what her brother has gone through, and she's grateful to Naruto for changing her brother and attempting to save him.
After arriving at Sunagakure, Team 7 learns of the attack on Kankuro. Before they can help, they are attacked by Chiyo, Sunagakure's resident poison specialist, who mistakes Kakashi for his father, Sakumo Hatake. Despite the failed attempt by the medics on-hand, Sakura cures Kankuro, thus demonstrating her skill with medical jutsu. Sakura is also able to develop several portable antidotes rather quickly. Using a piece of Sasori's clothing found on one of Kankuro's destroyed puppets, Team 7 is able to track him, thus leading them to Gaara. Temari offers to assist them, but Chiyo goes in her place since Chiyo is Sasori's grandmother, and Temari is left to guard Sunagakure's borders. Back in Konoha, Tsunade decides to send Team Guy as backup for Team 7.
As they approach Akatsuki's hideout, Team Kakashi is confronted by Itachi Uchiha while Team Guy fights Kisame Hoshigaki. Itachi catches Naruto in a genjutsu by merely pointing a finger. The genjutsu manifests as a vision of Sasuke, Sakura, Kakashi, and Gaara emerging from Naruto's body and taunting him, playing on his insecurities. Naruto tries to dispel the genjutsu by stopping his chakra flow (something he learned from Jiraiya) but fails. As Naruto breaks down in tears during this emotional assault, Sakura and Chiyo break him out of the genjutsu. Kakashi creates an opening for Naruto to use his Spiraling Sphere, or Great Ball Spiraling Sphere, to take out both Itachi and Kakashi's clone. However, Chiyo recognizes Itachi's body to actually be of Yura, a member of Suna's advisory council. He is revealed to be a double agent under Akatsuki's employ. A similar person is found by Team Guy after they defeat Kisame. Apparently, these two were used as body substitutes for the Akatsuki leader's Shapeshifting Technique.
The group surmises that this was just a delaying tactic to buy Akatsuki enough time to draw the Shukaku out of Gaara. Chiyo tells the group that if Shukaku is fully extracted from Gaara, he will die. Sakura cries, realizing that the same is true for Naruto. However, Naruto misunderstands and tells her not to worry because he'll save GaaraAt the grotto where Gaara is being held, the group figures out that a barrier jutsu has sealed off the entrance. Team Guy decides to remove the four seals protecting the cave, while Team Kakashi deals with Akatsuki. However, removing the seals triggers another delaying trap, causing Team Guy to confront clones of themselves. Inside the cave, Naruto and Kakashi find Deidara and Sasori guarding Gaara's lifeless body. While Chiyo and Sakura face Sasori, Deidara flies off on a clay bird with Gaara's body, with Naruto and Kakashi in pursuit.