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.

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.

Sai receives a chilling glare from Sasuke's Sharingan that frightens him. Sai gives Orochimaru a bundle with information about Konoha's ANBU. Yamato gives Sakura and Naruto seeds with his chakra that enables him to track them inside the lair, and reveals that he was able to track Sai because he put a seed in Sai's clothing and food during the visit to the hot springs. Kabuto locks Sai in a room, and the boy summons a bingo book from scrolls he carries. Yamato uses a jutsu to open a tunnel into Orochimaru's hideout, and he, Naruto and Sakura travel to Sai's room undetected.

Naruto, Sakura, Sai and Yamato head out for a new mission near the Fire Temple. When the other party fails to show up at the rendezvous point, the team gets separated and Naruto stumbles upon one of the four hidden tombs they came to protect. Due to a misunderstanding, he fights one of the monks-in-training from the Fire Temple, Sora, who also uses wind chakra based techniques. After the confusion, the monks and Team Kakashi travel to the Fire Temple, and Naruto recognizes it from his nightmare.

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.

Naruto proceeds to the next step of his training, the cutting of a waterfall. Hidan and Kakuzu reach the Fire Temple and fight Chiriku, so as to obtain the bounty on his head. After defeating him, they move out to claim the bounty and thereafter target the Nine Tails Jinchūriki Naruto.

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.

While Naruto continues his training with Gamakichi and Gamatatsu, Yamato, Sakura, and Sai prepare to leave and back-up Kakashi's group. As Guren and her gang prepares to intercept Kakashi's group, Yukimaru grows concerned for her safety and gives her a charm in hope of a safe return.

Naruto runs into Guren while trying to find Yūkimaru. Yamato and Kakashi find Naruto and bring him back to the group. Kabuto tells Guren that Yūkimaru is only a tool to control the Three-Tails, which upsets Guren. Meanwhile, Shizune, Ino, Tenten and Lee meet up with the team and tell them that their new mission is to rescue Yūkimaru and capture the Three-Tails before Orochimaru's group can capture it.

Kabuto plans on breaking Leaf’s The Four-Corner Sealing Barrier from the inside by using Yukimaru’s power and have the Three-Tailed Beast go on a rampage.

The Sealing Team prepared to start sealing the Three-Tails and tell Sai to take Yūkimaru somewhere safe, but he gets attacked by Kabuto's men. Kabuto meanwhile prepares his plans while Lee, Tenten, and Kiba are also attacked. Rinji finds his men and converts them back to his side, ordering them to attack the Sealing Team; they're stopped by Kakashi, Yamato and Shino. Rinji then makes Yūkimaru eat the pills to control the Three-Tails, which Naruto and Guren learn about.

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…

By using himself as an explosive, Deidara creates an explosion ten kilometers in diameter, something not even Sasuke will be able to escape from. Is this the end of Sasuke? Elsewhere, someone approaches the Akatsuki leader and gives him orders to catch Naruto himself. Who is this true mastermind of the Akatsuki plot lurking in the shadows?

Jiraiya realizes that the six Pains are all ninja he's met before. Putting various pieces of information together, Jiraiya figures out Pain's true identity, but Pain doesn't intend to allow Jiraiya to leave with that information alive. Elsewhere, the fated meeting between Itachi and Sasuke arrives, and Sasuke foresees Itachi's death.

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?

Pain confronts Tsunade and questions her about Naruto's whereabouts. Tsunade argues with Pain about his motives, but Pain soon gets the info he needs from another source. Before preparing to depart, Pain unleashes a devastating attack on the village! Meanwhile, Naruto prepares to return to the Leaf Village, but he may be too late.

Nagato reveals the truth about what happened to Yahiko and what made him disregard Jiraiya's ideals. With his story done, he demands to hear Naruto's answers. Will Naruto's answer be enough to convince Nagato to stop his evil plans, or will Naruto be forced to kill Nagato?

As the ninja of the Hidden Leaf Village work on repairing their village in the aftermath of Pain's invasion, Naruto and Sakura come across a familiar face among the carpenters: Inari and Tazuna have arrived to help out. Inari recalls what happened after Gato's death and how Naruto and Sasuke came to his rescue.

During the two-and-a-half-year time period in which Naruto was training under Jiraiya, the latter decided that it was time for Naruto to learn how to repel genjutsu. During this training session, the two traveled to a village which Jiraiya had previously been associated with, but they discovered that something dark was amidst.

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.

Karui decides to get information about Sasuke from Naruto by any means necessary. When Naruto refuses to sell Sasuke out, Karui takes out her frustration upon the former. Meanwhile, Danzo prepares for the Kage Summit, and determines to keep Naruto confined to the Leaf Village.

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?

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.

Tsunade sends out Naruto under the guise of a top-secret mission to keep him hidden away from the Akatsuki. Unfortunately, Naruto, Yamato, Gai, and Aoba are stuck at the pier due to a report of a monster attacking ships.

Shikamaru begins to feel the pressure of shouldering the lives of his friends in the upcoming Fourth Shinobi World War. To help ease his mind, Shikaku sends his son along with Tenten on a mission to Mokuzu Island to replenish supplies.

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.

Kiba trains hard to catch up to Naruto, who is now hailed as the hero of the Leaf Village, but with little success. Feeling desperate, Kiba asks Kakashi if he could train him.

Minato is forced to use his Flying Raijin jutsu and leave his wife Kushina behind to save their newborn son, Naruto, from a masked assailant.

Kakashi becomes part of the ANBU Black Ops, an elite team of shinobi who are under the direct command of the Fourth Hokage, Minato Namikaze.

After being saved by the target he was ordered to kill, Tenzo realizes that the man known as “Kakashi the Friend Killer” is someone who values the lives of his comrades more than anyone.

Madara and Hashirama eventually become the leaders of their respective clans.

An ancient ruin in Demon Desert comes crumbling down during the battle for the scrolls.

The Tsuchikage and Raikage, who are in the Leaf Village to attend the Five Kage Summit, mention that they have already prepared wedding gifts for Naruto. Gaara finds himself in a dilemma. He's advised that the gift should be something that befits the Kazekage. He also learns that the Raikage is planning to perform a dance. Kankuro chimes in and suggests Gaara should dance as well—further plunging Gaara into indecision.

Naruto had once lived a lonely existence, ostracized by everyone. But Iruka's words and his very presence have supported Naruto to this day. As Naruto's wedding nears, Iruka begins to lose sight of what he was to Naruto, and is unsure of what to say for his message.