Gaara, his strength completely exhausted, is whisked away by Deidara. Kankuro ignores Baki’s efforts to stop him and immediately sets out in pursuit with a platoon to rescue Gaara.

Granny Chiyo and Sakura rescue Naruto from Itachi’s genjutsu. Without a moment’s delay, Kakashi begins a counterattack.

Chiyo and Sakura take cover, and Sasori wastes no time unleashing a ruthless attack.

Naruto loses all reason to anger and is gradually taken over by the Nine-Tailed Fox Spirit. Having been forewarned by Jiraiya, Kakashi narrowly manages to suppress the Nine-Tailed Fox.

Naruto, Choji and Shikamaru attempt to capture and interrogate Sai, but Sai withdraws after insulting Naruto. Shortly afterward, Ino appears. Concerned that the demon fox 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 upon Sai's appearance.

Kabuto comments that Naruto's state is a consequence of his desperation to bring back Sasuke. Sakura begins to cry and approaches Naruto but is injured when his attention turns to her. Yamato uses the mokuton jutsu to bind Naruto before he does any more harm. Kabuto heals Sakura, reasoning that the Konoha ninja are not Orochimaru's enemies because they are also fighting Akatsuki. Yamato uses the abilities of the 1st Hokage to forcibly return Naruto to his normal state. Meanwhile Sai confronts Orochimaru with a message from Danzo. Orochimaru responds by piercing Sai with Kusanagi.

As Team Kakashi continues their search for Sasuke, Naruto suddenly collapses due to his previous fight with Orochimaru. As Naruto wakes up, Sai begins to reveal more about his brother, but Orochimaru suddenly attacks them. Sakura and Yamato come to Naruto's aid against Orochimaru, while Sai continues the search. Just as Sai finds Sasuke, Yamato finds Sai's bingo book with Sasuke listed as a target for assassination.

Naruto and his clones continue to work on chakra nature manipulation by slicing leaves. After some struggling, Naruto approaches Asuma, who is also a wind type, for advice, after which Asuma gives Naruto's clone a few pointers. Naruto is subsequently able to slice a leaf in half. Asuma and Yamato head out with their teams on new missions. It is revealed that Asuma is the Third Hokage's son and that he is in a relationship with Kurenai. Meanwhile, on a hill overlooking a burnt village, four cloaked figures discuss the awakening of the Fire Country by eliminating the Leaf Village.

Danzou is brought in for questioning after being caught meeting with a young Rain ninja. Sora confronts Asuma, and Asuma admits to having killed Kazuma. He attacks Asuma, his arm once again assuming a demonic form. Afterward, Naruto gets injured while shielding Sora from the attacks of an unknown individual, presumably from Root. Furido then approaches Sora, telling him to kill both Asuma and the Hokage to avenge his father. Later on, Naruto catches Sora going after Tsunade. Sora retreats as Shizune and a few other ninja arrive, but Naruto pursues him. At that moment, a mysterious lightning storm strikes, cutting off power to the entire village.

Konoha's ninja fight off the revived zombie members of the Kohaku clan. The four Guardian Ninjas, Seito, Tōu, Nauma and Kitane, are also revived. Asuma realizes that they are planning to use Limelight, a jutsu in which the four create a lightning blast powerful enough to destroy Konoha. Asuma sends Sakura and Yamato after the other three while he remains behind to battle Kitane, but Fuen tackles Sakura and Fudo fights Yamato. Meanwhile, Naruto catches up to Sora, but Sora runs off in search of Furido. Naruto tries to pursue him, but is assailed by Fuuka. Soon after, Sora reaches Furido, who admits that he had planned to destroy Konoha.

Asuma apologizes at the grave of the Third Hokage for not understanding his advice concerning what the "king" of the Fire Country is. At the hospital, Naruto and Sai recover, despite Naruto's desire to resume his training. Tsunade receives a report from Kakashi that Akatsuki is on the move. Elsewhere, Yugito Nii, the Two Tails Jinchūriki, struggles against Hidan and Kakuzu and unleashes the Two Tails, but is defeated and captured. Hidan and Kakuzu then turn their attention to the Fire Country for their next target.

Guren is rendered unconscious and relives her past as Naruto is caught in an illusion about Sasuke. After Kakashi finds him, Teams Kakashi and Kurenai conclude the mist around them causes Genjutsu courtesy of the Three-Tails. After Guren wakes up, Yūkimaru suffers another fever and passes out. Tsunade hears of the Three-Tails and assmbles Shizune, Ino, Tenten and Lee to go and seal it before the Akatsuki do. Naruto and Sakura talk about the home that people should return to before Naruto heads off to find Yūkimaru.

Orochimaru's body has reached its limit and the time for the ritual has come. Sasuke has other plans, however, and seeks to target a bedridden Orochimaru.

Over ten years ago, the Five Great Nations’ were in the midst of the Third Great Ninja War. Future Fourth Hokage Minato Namikaze assigns young Kakashi, Obito of the Uchiha clan, and Rin, on a mission to Kannabi Bridge...

While the members of Team Hebi head towards Itachi's location, Jiraiya infiltrates the Hidden Rain Village in hopes of gathering information on the Akatsuki leader. Jiraiya captures two Rain ninja and interrogates them about Pain, but what he learns shocks even him.

After the peformance of the forbidden jutsu, Hotaru is horrified to see the damage the jutsu has done. Shiranami then notices the forbidden jutsu overflowing with chakra and the fact that it would destroy itself along with Hotaru. While Naruto chases the fleeing Shiranami, Utakata tries to save Hotaru using the hidden power within him. Can Utakata save Hotaru?

Team Kakashi returns to the Hidden Leaf Village after completing their mission. As Naruto thinks back to the talk he had with Itachi, he's summoned by Tsunade, where he discovers shocking news regarding Jiraiya.

The Fourth Hokage, Minato Namikaze, left behind his legacy before he passed away. Naruto, Sakura, and Sasuke attempt to find Minato's legacy before the other shinobi teams can get to it.

After discovering a kunai knife with a secret message on it, Naruto winds up being pursued by three kunoichi from the Hidden Waterfall Village. Iruka mangaes to find him, but when the situation grows worse, Kakashi appears to save them both.

After having discovered that the village was under the control of rebels from the Hidden Rain Village, led by Hanzo, Naruto and Jiraiya decided to take action to help save the women and children taken hostage and free the village from the Rain's tyrannical control.

The time has come for each Kage to leave for the Kage Summit in the Land of Iron. On his way to the meeting, Danzo gets attacked by shinobi from the Wood Country who want to take his head. Meanwhile, Naruto, with Kakashi and Yamato by his side, heads off to find the Raikage to convince him to spare Sasuke.

As he is resting, Naruto starts dreaming his past experiences with Sasuke that made the two friends closer. When he tries to follow Kakashi, who is in pursuit of Sakura, he is stopped by Yamato, saying that he has orders from Kakashi to return Naruto to Konoha. Naruto devises a plan to sneak out and leaving a shadow clone to fool Yamato. He goes into Sage Mode to locate Kakashi. He then starts remembering the experiences that brought Sasuke pain in his life. Naruto decides what he can do for Sasuke if they come face to face.