Immediately after Yamato signals Naruto and the others out to the bridge where Orochimaru and Kabuto are waiting, Naruto's chakra begins to boil with the chakra of the Nine-Tailed Fox. Slowly, Naruto grows more tails as Orochimaru taunts him and makes him even more angry. Meanwhile, Yamato remembers Jiraiya speaking of how many tails he has seen Naruto grow. Jiraiya explains more about what happened and more about how Naruto acts when he's in his Nine-Tails form.

Yamato and the team enter Sai's room and confront him while Kabuto makes his way there as well. Sai tells Team Kakashi that not only was he to help with Konoha's destruction but also act as a spy against Orochimaru. Yamato reveals the secret of "Root"- its members were trained like Kirigakure's students in that they had to kill their friends so as to eliminate their emotions. Sakura returns Sai's book to him, remarking that he still has emotions because he treasures it. Sai then tells the group about his bond with his brother. Finally the team decides what to do about Sai's betrayal outside the lair. In doing so, Naruto tells the group about his own bonds and about how far he's willing to go to bring Sasuke back.

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.

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.

A call from the Akatsuki leader forces Hidan and Kakuzu to fall back, but in the wake of the aftermath, not everyone makes it back to Konoha alive.

In the aftermath of the battle, Teams 7 and 10 return to Konoha. After examining Naruto, Tsunade officially classifies Naruto's new technique as a Forbidden Jutsu and warns Kakashi never to let him use it again. What is the terrible secret of the Rasen Shuriken that has left even Tsunade stunned by its power? Meanwhile, Orochimaru orders Kabuto to search for a woman who will help him reach his goal.

Naruto successfully breaks down the crystal labyrinth with his new jutsu and he and the rest of Team Kakashi come to Kakashi, Kiba and Shino's aide, and rescue Hinata as well. Meanwhile, Kabuto, Guren, Yukimaru and Gozu head to the lake Kabuto and Yukimaru went to before. What could be in the lake that Orochimaru wants?

Yūkimaru falters and the Three-Tails injures Guren. Rinji tells Yūkimaru to suppress the beast to save her, but he is unable to do so. Guren leaves her position and protects Yūkimaru with a Crystal Style shield. Naruto goes out to find Yūkimaru, but ends up fighting the Three-Tails with Guren. Despite their efforts to defeat it, the beast overpowers the two of them, and then it proceeds to swallow them. Meanwhile, Kakashi, Shino and Sai find Yūkimaru unconcious and flee with him, leaving Kabuto frustrated.

Orochimaru reveals the true, hideous form his body has taken from years of experimenting on his body. Can Sasuke defeat this menacing form, or does Orochimaru still have a few tricks up his sleeves?

Kakashi splits the two teams into five separate groups, each aided by a couple of his ninja dogs, in order to locate clues about Itachi and Sasuke's whereabouts. Unbeknownst to everyone, familiar foes have set their eyes upon both Naruto's group and Sasuke.

Having suspicions about the Nine-Tails' attack on the Hidden Leaf Village years ago, Jiraiya tells one of his frogs that the time may come when Naruto will need to access the fox's full power. His interrogations finished, Jiraiya sets out in search for Pain, but winds up encountering Konan instead. Is there a connection between Jiraiya, Konan, and the mysterious Pain? Elsewhere, one of Naruto's shadow clones runs into Team Hebi.

As Sasuke has finally fulfilled his goal in killing Itachi and avenging his clan, he collapses from exhaustion. The news of his victory reaches the Leaf ninja and Tobi, who both race towards Sasuke's location. What does Tobi plan to do with him and who will reach Sasuke first?

As Naruto heads back to the Tsuchigumo Clan village, Akaboshi and his group find Hotaru with the help of Hotaru's uncle. Hotaru manages to escape but the ninja bandits surround her in the forest. Utakata comes to her aid and manages to take her and escape from the ninja bandits. Akaboshi and his group are about to chase after them until their boss arrives and reveals to them that Utakata is in the Hidden Mist Village's Bingo Book.

After reading Jiraiya's first book, Naruto becomes more determined than ever to complete his training. Elsewhere, the angered Raikage plans to call all of the kage together for a meeting.

Pain's God Realm finally enters the battle. As Naruto's toad allies fall one by one, the situation begins to look grim. Can Naruto defeat Pain?

Deciding to believe in Naruto, Nagato uses the Gedo Art: Rinne Rebirth jutsu, expending the last of his chakra, and thus giving his life, to revive every person in the village who died in the attack, saying that it's the least he can do. With Nagato dead, Konan leaves Akatsuki, taking Nagato and Pain's God Realm (who is actually the body of Yahiko) with her, parting with Naruto saying that since Nagato believed in him to achieve true peace, she will as well. As Naruto returns to the Leaf, he is astonished to find the entire village awaiting his return, hailing him as a true hero. After all these years, Naruto has finally received the acknowledgment he's always wanted.

The ship is caught in a storm and Naruto uses his shadow clones to protect the ship.After the storm, Naruto wakes up and a quarrel begins between Naruto and his Shadow clones. Soon his shadow clones revolt and take control of the ship and the crew is forced to land on a nearby island. Naruto is taken hostage by the shadow clones and they put forth their demands to him. Naruto is saved by Yamato and the others only to find that it was a dream. It was caused when a Shadow clone was released and the memories of it returned to Naruto. Naruto then realizes the worth of his clones and releases them.

Ino sees Sakura falling from the sky. Although she manages to save her, the shock of the fall has left Sakura with amnesia.

Naruto and Killer Bee engage in battle against the reanimated Itachi Uchiha and Nagato. Itachi learns from Naruto that Sasuke has chosen the path of vengeance.

Kakashi visits the Uchiha District and notices that the community seems more antisocial than the last time he visited. Meanwhile Itachi finds concrete evidence regarding the Uchiha Clan’s coup against the Leaf. The fateful moment is fast approaching…

Villages did not exist when Hashirama was a child. It was during this strife-filled time that he met Madara Uchiha.

Madara now possesses the Rinnegan in both eyes, and he is the strongest, most despicable enemy the newly reunited Team 7 has ever faced. Kakashi calls upon Team 7 to recall their first lesson with the bells, and to use teamwork!

The Masked Man shows Neji and Naruto images of past incidents that occurred in the Leaf Village. Meanwhile, Shikamaru and friends join up with Team Jiraiya to rescue the children. After fighting side by side with the Leaf, Yahiko and the others seem to have a change of heart.

The Anbu who attack Naruto and Shikamaru are agents sent by Danzo, who had promised Orochimaru that he would deliver Sasuke safely to him. Luckily, Neji, Lee and Tenten rush to their aid in the nick of time! Meanwhile, Hiruko reveals the truth behind the incident involving Hizashi

Itachi accompanies his friend Shisui on a three-part training exercise. The two come across a battle between the Hokage’s ANBU and the Foundation. Itachi is confused by their motives and can't discern which side is right or wrong. But Shisui is unwavering in his determination to stop the fighting.

Kaguya is furious that Hagoromo has broken the law. Hagoromo finds out what Kaguya did in the past and makes up his mind to fight her. Knowing nothing about her, Hagoromo cannot trust her—he wonders if the love and the despair she experienced are the sole cause of her anger. Unable to reach an understanding, mother and sons begin their long, sad battle.

Everyone believes that Indra is the best choice to be Hagomoro's successor, and the sage's indecision begins to cause anxiety among his followers. Finally, Ashura returns home, and Hagoromo reveals who he has chosen.

The super-secret mission to find Naruto and Hinata a wedding gift proves to be difficult for Shikamaru. Choji has found the perfect gift, which adds to Shikamaru's panic. But then Choji mentions something in passing and Shikamaru gets an idea. All he needs now is to enlist Temari's help!