Naruto and Sakura defeat Kakashi in the survival challenge. Tsunade assigns them to a three-man squad led by Kakashi, who tells them they are now his equals.

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

Guy prepares to use a forbidden secret jutsu. Meanwhile, Naruto falls under Itachi’s genjutsu, and all the anti-genjutsu training he underwent with Jiraiya races through Naruto’s mind.

Granny Chiyo and Sakura manage to expose Sasori, who amazingly looks no older than he did twenty years earlier.

Sakura and Granny Chiyo are engaged in a fierce battle with Sasori, who is able turn himself into a human puppet. They somehow bring Sasori down within the time limit, but he ends up reviving.

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.

Naruto continues to get even more enraged and easily counters Kabuto's attack, flinging him away. Naruto's counter throws Kabuto into Sakura, knocking her unconscious. Orochimaru continues to watch Naruto become more enraged, eventually destroying the Bridge of Heaven and Earth. As the bridge collapses, Sakura slides off the edge. Sai draws a bird to fly, but chooses to follow Naruto and Orochimaru instead of saving Sakura. Yamato saves her at the last second, and creates a wood clone to catch up to the battle. Eventually the fourth tail appears, allowing the vile chakra to completely control Naruto's body, forming him into a miniature Nine-Tailed Fox.

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.

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.

Asuma supervises Naruto and Sora's wind chakra training, and notices that Sora, like Naruto, has very powerful chakra. Tsunade and Yamato learn from Chiriku that Sora was inadvertently responsible for an incident in which the Temple of Fire was destroyed. Later, Asuma gives Sora a claw made from the same materials as his chakra blades. It is revealed that Asuma killed Sora's father Kazuma, who had planned to kill the Hokage. Furido then approaches Sora, telling him that Asuma is responsible for his father's death and passing him two "king" pieces from a Shogi set for Asuma. Danzo mysteriously disappears. Naruto approaches a furious Sora in the training grounds, who easily throws a chakra-powered kunai through a tree and destroys the stone behind it.

Sora refuses to let Furido destroy the village despite his grudge against Asuma and the Hokage. He is beaten up by Furido, who claims that his father had a similar flaw. Asuma gets trapped by Kitane in a force field of lightning. Meanwhile, Yamato and Sakura kill their opponents, and Shikamaru heads to the battlefield with a plan to defeat the zombies. Just as he puts it into motion, however, Fuen's barrier falls and Fudo's revival technique ends, and the zombies turn to dust.

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 mourns Chiriku's death, and realizes that Hidan and Kakuzu are trying to claim the bounty on his head. Meanwhile, Hidan and Kakuzu take Chiriku in for their payment. Meanwhile, Kakashi shows Naruto what the true goal of his training will be.

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.

While Akatsuki discusses the true goals of their organization, Naruto continues his training. Meanwhile, Tsunade receives the tragic news.

All of Konoha mourns the tragic loss of Asuma Sarutobi. Knowing that Hidan and Kakuzu are bound to return, Shikamaru, Choji, and Ino prepare to head off to take revenge upon the duo while Kakashi takes temporary leadership of the team.

Naruto challenges Kakuzu with his new technique, the Rasen Shuriken, but can he defeat Kakuzu when his technique isn't even complete yet?

As Naruto recovers from his injury, Kakashi prepares to tell him the grim news about his new technique. Meanwhile, Sasuke secretly trains and has an encounter with a strange young girl.

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.

In Konoha, Tsunade discovers they have an enemy using Crystal Style. While on his mission with Team Kakashi, Naruto meets Yūkimaru once again and talks to him. Guren puts a gigantic Crystal Prison over the forest trapping Team Kurenai inside. Guren then prepares six Crystal Clones and attacks Team Kurenai with them. Hinata defeats one clone but is locked up in a Crystal Prison by another. Team Kakashi reaches the borders of the giant prison and Naruto uses his new Jutsu with Gamatatsu to bust a way in.

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.

The sealing team continue their efforts to seal the Sanbi while Kakashi and the others face against a monster fused together by Kigiri, Nurari and Kihou. Kabuto reveals Orochimaru's plans involving the Sanbi and he and Naruto begin to fight. While protecting Yukimaru, Guren fights against the real Rinji, who has been resurrected by Kabuto. When Guren sacrifices her life to save Yukimaru, Yukimaru's powers go into full effect. Now, in order to protect Yukimaru, Naruto prepares to go against the rampaging Sanbi.

After Sasuke reverses Orochimaru's body-switch with his Sharingan, he releases one of Orochimaru's test subjects, Suigetsu. Determined to put together a team to achieve his goals, he decides to request Suigetsu's assistance. Suigetsu agrees, but only if he's willing make a detour to the Land of Waves first.

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.

After successfully breaking out of Itachi's Tsukiyomi, Sasuke gains the upper hand on his weakened brother. With no other alternative, Itachi activates his second Mangekyo ability, Amaterasu, a black flame said to burn forever.

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.

After failing to bring back Sasuke, the Leaf ninja start heading back to the Hidden Leaf Village. Tsunade, however, sends Katsuyu to inform them that the barrier of Mount Katsunagi of the Tsuchigumo Clan, which holds a powerful forbidden jutsu, is broken. While Kakashi and Team 8 head back to the Leaf Village, Team 7, lead by Yamato, must check out what events are taking place.

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?

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.

In a flashback of Naruto and Sakura's, Team 7 is on a mission to take an ostrich called Mr. Ostrich to his home. They arrive at a village where they see a swordsman named Tsukado who has a vendetta to carry on a man named Katazu who killed his distant relative Shikazo. Tsukado fails to defeat him so Naruto decides to teach him unusual revenge lessons. Katazu has then took his brother's identity and attracted Shikazo's pursuers while Kageki and his family went into hiding. Tsukado decides not to kill him and ends their years of fighting though Kanabun wants them to keep fighting. The swordsmen, Team 7 and Mr. Ostrich chase the Kanabun Gang out of town.

Naruto and Sakura learn that Danzo has been made Hokage and that his first order is to eliminate Sasuke. The two go to Sai and inquire about Danzo, but Sai reveals that a curse mark given to all members of the Foundation prevent him from revealing anything about the new Hokage. Soon afterward, Karui and Darui attack them, demanding information about Sasuke.

Madara brings Sasuke out of his dimension to battle Danzo. When Sasuke demands answers concerning Itachi, things turn ugly, and Danzo reveals a few tricks he has up his sleeves (literally). What is Danzo's true strength, and can Sasuke summon enough power to suppress it?

As Naruto and Sasuke clash, their Rasengan and Chidori explode, sending them both flying. When Zetsu and Madara appear to aid Sasuke, they decide to retreat to the Akastuki headquarters. Before they leave, however, Naruto has one last thing to say to Sasuke; something that will have an impact on both of their lives.

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.