A figure passes through the gates. It's an older Naruto, who has returned from a long training journey with Jiraiya. Naruto Uzumaki is back!

On her way to the Sand Village, Temari encounters Kakashi and his team. Kakashi admonishes Naruto when he tries to rush ahead…

Teams Kakashi and Guy take a short rest. Granny Chiyo watches Naruto dozing off and is reminded of Sasori as a child. The pursuit resumes, and when Chiyo wonders why Naruto puts such effort into...

Sakura destroys the Third Kazekage puppet thanks to a secret antidote she had taken.

Teams Kakashi and Guy 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.

Kabuto creates a fake corpse that resembles Sai, containing hidden traps to slow down Yamato's clone after sensing it. Naruto hasn't completely recovered from using the Demon Fox's chakra, and Yamato says that he will be left behind if he cannot keep up. Naruto is determined to finish his mission and not slow the team down. However Team Kakashi is forced to take a break when it's clear that Sakura has not fully recovered from her own injuries. Yamato then uses this opportunity to talk to Naruto alone and reveals to him that the one who hurt Sakura was Naruto himself. Naruto is shocked by what Yamato says to him.

Orochimaru and Kabuto convince Sasuke to withdraw with them, and Naruto weeps over his failure to return Sasuke to the village, but Sakura reassures him that they will bring Sasuke back together. Naruto's team reports to Tsunade about the results of the mission, and Tsunade is greatly angered over Danzo's scheme, particularly his leaking classified information to further it. Sai asks Danzo to allow him to remain with Team Kakashi, and Danzo reluctantly agrees. Sai goes on a mission with his team, having come to see them as his friends.

Tsunade suspects that Danzou is plotting something and orders an investigation of him. Team Kakashi, Chiriku and Sora notice the coffins moving on their own, but fail to intercept them. The coffins emerge on a cliff, where the leader of the enemy ninja orders his subordinates to deal with their foes. The ninjas turn the area into a maze of rocky canyons and pits, full of deadly traps. The team members are separated from each other, and begin facing off against the enemy. Yamato speculates that the ninja may have orchestrated the theft in order to target someone on his team.

With Konoha in complete darkness, the village struggles to defend against the four attackers who have sealed the entire village behind a barrier. The entire village is in a state of emergency. Asuma, commanded by Tsunade to follow Sora and Naruto, finally catches up to them. Asuma realizes that the four invaders plan to annihilate the entire village using the lightning powers of the corpses that they stole. The revelation shocks Sora. As Asuma leaves to help hold off the attackers, he instructs Naruto to continue pursuing Sora.

The struggle between Naruto and Sora continues. Asuma and Kazuma fight. Sai arrives, having snuck out of hospital, and binds Kazuma with an ink snake. Kazuma breaks out of Sai's jutsu and charges Asuma, but is killed. Naruto eventually reaches Sora, who manages to release the Nine Tails's chakra. Sora then leaves the village to travel the world. Asuma and Shikamaru play shogi and discuss who the king of Konoha is. Elsewhere, two Akatsuki members, Hidan and Kakuzu, appear chasing the Two Tails Jinchūriki.

Asuma’s team reaches the bounty station and ambushes Hidan. Izumo and Kotetsu attack Hidan, but are unable to kill him despite stabbing his vital organs. Asuma tells his teammates that if they retreat they will be killed and Konoha will be endangered. Shikamaru realizes that Asuma is considering sacrificing himself to help defeat the enemy, based on what he knows of Asuma's shogi strategy. Asuma begins fighting Hidan, while Shikamaru distracts him by forcing him to dodge Shadow Sewing. Hidan cuts Asuma on the cheek and steps into a circle of blood as Asuma uses a jutsu to engulf Hidan in a cloud of ash. Asuma then sets the cloud ablaze, supposedly killing Hidan.

Shikamaru continues his fight with Hidan. Hidan manages to injure Shikamaru and curses him the same way he did Asuma, but when Shikamaru survives Hidan's attack, Hidan realizes something isn't quite right.

Naruto runs into unexpected difficulties as he trains with Gamakichi and Gamatatsu. While Kakashi's group searches for Guren and her gang, Yukimaru seems to develop interest in Naruto.

Yūkimaru summons the Three-Tailed and immobilizes it while Guren tries to capture it. It manages to break free and attack. Kakashi tells Naruto to investigate the lake, while they find Rinji and the others. Rinji and his men prepare an ambush, but Hinata, Sakura, and Sai arrive to avert it. Naruto summons Gamakichi and Gamatatsu and approach the Three-Tails, where they see Yūkimaru and learn of his allegiance to Guren. Trying to save Guren, Yūkimaru tries to suppress the Three-Tails once more, before managing to escape with her.

The sealing unit prepares the sealing barrier and the other two teams go into battle with Guren and her henchmen. Kakashi, Naruto and Sai stall Guren and Gozu while Shino prepares to go against Guren's crystal style. Meanwhile, Lee goes against Guren's other henchmen and gets trapped in their smokescreen. Can Lee find a way to defeat them?

Obito ignores Kakashi’s order to continue with the mission and leaves to save Rin, who was kidnapped by the Rock ninja. But the enemies detect Obito’s arrival and defeat him. Kakashi arrives at the last minute and saves Obito…

Sasuke's long awaited battle with Itachi begins with the Uchiha brothers throwing genjutsu after genjutsu at each other. Sasuke seems to have Itachi cornered and asks him a few questions of the Uchiha massacre. Is Itachi not the only one involved in the Uchiha massacre? And does Sasuke still not possess enough hatred to defeat Itachi?

Sasuke fights Killer Bee and is injured by his swords. Karin heals him, and Sasuke, Suigetsu, and Jugo then begin a combined assault on Bee until he decides to use the Eight-Tails' power. Sasuke is injured and revived again by Jugo, who regresses in age as a result. All healed, Sasuke unleashes Amaterasu on Bee, finally able to subdue him. Meanwhile, two Cloud ninja watch the fight from a cliff, and they notice the Uchiha crest on Sasuke. They rush the news to Bee's big brother, the Raikage.

Naruto, Sai, and Yamato arrive to save Hotaru and Utakata from the attacking ninja who they discover are Anbu from the Hidden Mist Village. Yamato attempts to negotiate alone with the head of the Mist Anbu, Tsurugi, and after their discussion, Tsurugi talks to Utakata alone. Tsurugi attempts to convince Utakata to return to the Hidden Mist Village but the latter refuses and remembers the horrible pain he suffered at the hands of his former master.

Shikamaru tries to decipher the dying message Jiraiya left before his death but cannot figure out what it says. Shikamaru asks for Naruto's help, thinking he might know the code. Can the saddened Naruto decipher Jiraiya's dying message?

While she and Neji prepare to visit an old man who makes ninja weapons, Tenten remembers the first time she visited him alongside Naruto and Neji. Utilizing a strange new weapon she had never seen before, Tenten fought against two ninja who had stolen two of the man's powerful weapons.

A female spy, Hanare, from the Hidden Lock Village (Land of Key) is caught by ANBU pretending to be a musician. She is interrogated. However, the interrogation proves unsuccessful. Slowly, her past is revealed and so is her relationship with Kakashi. Team 7 spy on the two as they go around town, under the impression that the two are dating. After The Lock Village keeps a Leaf Village ninja hostage, they exchange Hanare for the ninja. It is then revealed that Hanare has a special ability, causing a large chase to occur. In the end, Kakashi lets Hanare free. The musician seen at the beginning entertaining Konoha ninja reminds Kakashi of Hanare which prompts the flashback.

Naruto thinks back to the time when he encountered the soul of a man named Kisuke. Kisuke didn't recall anything about who he was, but a visit to the Leaf Village's hospital revealed something startling. Meanwhile, higher-ups of the Fire Country met to decide on a new security system for the Leaf Village put together by a ninja named Sabiru. Who exactly were Kisuke and Sabiru, and what connection did the two have?

Without any warning, Zetsu bursts through the floor in the middle of the Five Kage Summit and announces that Sasuke is somewhere in the vicinity. The Summit is immediately put on hold, and the Kages and samurai begin searching for him. Meanwhile, Naruto receives an unexpected visit from Madara, who says that he needs to talk to him. How will Sasuke respond to being discovered, and what are Madara's intentions?

While talking with his students, Shino talks about how he and his team got together and became more close as friends and teammates. The story switches to Shino's flashback during the first part of Naruto. They are on a mission assigned by Kurenai in which a Jonin assassin from a neighboring village. Shino gets defeated because of weak taijutsu and descends into depression. He even reveals he was going to abandon the team that helped him because he didn't think he was useful to them. But after his friends get in trouble with the rouge Shino comes back and defeats the rouge.

The legendary Ama no Hoko imbues the Nine Tails’ clone with enough power to destroy the world. Naruto is overcome by its immense power and lies unconscious.