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.

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...

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

Sakura hurries to get to Naruto with Granny Chiyo, who is suffering from the poison. The members of Team Guy rush to assist Team Kakashi. Meanwhile, with all preparations complete, Kakashi reveals his Mangekyo Sharingan.

Yamato disguises himself as Sasori after creating a wood replica of Hiruko, and goes to meet the spy. The spy turns out to be Orochimaru's right-hand man, Kabuto Yakushi, who reveals the location of Orochimaru's current hideout to Yamato. Orochimaru interrupts the meeting, appearing to attack Kabuto, and while it initially appears that Orochimaru has come after Kabuto, Kabuto attacks Yamato and reveals that he is truly loyal to Orochimaru. Orochimaru calls out Naruto, Sakura and Sai from where they are hiding and observing the meeting, and prepares to fight the team.

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.

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.

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.

Furido releases Sora's seal, and tells him the truth: Sora is a pseudo-Jinchuuriki. The chakra that had leaked from the Nine Tailed Fox when it attacked Konoha 15 and a half years ago was harvested and implanted into Sora. Just then, Asuma arrives at the scene with Naruto. Asuma recognizes Furido and it is revealed that he is Kazuma, Sora's father. Yamato, Sakura, Kiba, Lee, Ino, Choji and Shikamaru also turn up. Enraged, Sora wants to destroy everything, and turns into the Three-Tailed form of the Nine-tails. However, Yamato is unable to restrain him, because he does not have the First's necklace on him.

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.

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.

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.

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.

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.

Having become genin, Jiraiya, Tsunade, and Orochimaru are assigned to the future Third Hokage's platoon. Watching Sarutobi's space/time ninjutsu, Jiraiya becomes absorbed into learning it. One day, Jiraiya loses his way and stumbles upon Myouboku Mountain. There he meets the Great Toad Sage who predicted his arrival. See the origins of the Toad Sage Jiraiya!

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.

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.

Naruto manages to find Shiranami's location but he discovers that the Shiranami he found was actually the ninja bandits disguised as him. Hotaru finds the real Shiranami where the latter convinces Hotaru not to have the forbidden jutsu removed, and takes her back to the Tsuchigumo Village. After Naruto is saved by Utakata from the ninja bandits, the two return to the Tsuchigumo Village, where they find that Shiranami has everyone in the village under his control.

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.

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.

Back before Rock Lee had his surgery, Naruto, after donning the suit given to him by Guy, set out on a mission with Sakura and Ino to obtain a special flower which was a necessary ingredient for Lee's medicine. When Naruto picked one of the flowers, however, he had to face a strange technique that had taken on the form of Gaara.

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.

One of Sai's clones tells Naruto the truth surrounding Sasuke, something that Sakura couldn't bring herself to do. Before Naruto can even comprehend what Sai just said, they are interrupted by Gaara. What additional bad news concerning Sasuke does Gaara bring for Naruto?

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.

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.

Inside his mind, Naruto continues his battle against Nine Tails to take control of its immense power.

Zetsu reports on new intel from Kisame and Madara learns about Naruto hideout. Tsunade, Gaara, Lord Raikage, and others must figure out how to get Naruto out of the secret island of Land of Lighting and all without telling him about the war. New mission is introduced.

Kankuro’s commando unit enters enemy territory to set up a stronghold for the Allied Shinobi Forces. They are immediately ambushed by the Akatsuki’s own commando unit comprised of the reanimated Deidara and Sasori.

The Ino-Shika-Cho trio is ordered by Shikaku to take down the reanimated Asuma. Remembering Asuma’s final words, Shikamaru and Ino are determined to stop their former teacher.

Naruto finds himself inside Four Tails’ inner world, where he promises to free Four Tails from Madara’s control. Listening in on their conversation, Nine Tails recalls all the time he has spent sealed inside Naruto.