The temple monks explain that the tombs hold the loyal bodyguards of Fire Country's feudal lord. Naruto observes Sora sparring with other monks and becomes offended upon realizing he is holding back. Naruto challenges Sora, but just as the matter is about to get serious, another monk stops him. Naruto realizes Sora is despised by the other monks as he was himself and wishes to befriend him. Naruto visits Sora again and observes him practicing his wind jutsu in earnest, hoping to get strong enough to avenge his father. They later return to the temple to receive news that another tomb has been robbed.

Konoha's ninja fight off the revived zombie members of the Kohaku clan. The four Guardian Ninjas, Seito, Tōu, Nauma and Kitane, are also revived. Asuma realizes that they are planning to use Limelight, a jutsu in which the four create a lightning blast powerful enough to destroy Konoha. Asuma sends Sakura and Yamato after the other three while he remains behind to battle Kitane, but Fuen tackles Sakura and Fudo fights Yamato. Meanwhile, Naruto catches up to Sora, but Sora runs off in search of Furido. Naruto tries to pursue him, but is assailed by Fuuka. Soon after, Sora reaches Furido, who admits that he had planned to destroy Konoha.

The second stage of Naruto's training continues, while Tsunade sends out twenty teams composed of four ninja each to deal with the Akatsuki members in the Fire Country. Shikamaru leaves with Asuma, Izumo and Kotetsu, whereas Ino and Choji leave with Raido and Aoba. After putting in considerable effort, Naruto clears the second stage of his training, but collapses from hunger and exhaustion almost immediately afterward.

With careful planning, the group manages to find and trap Hidan and Kakuzu. However, things seem to be going a bit too smoothly.

Kabuto and Yūkimaru travel to a lake, where Kabuto attempts to draw out a mysterious creature. Guren branches off from her men to find Orochimaru, who has Sasuke fight an army of Sound Ninja as training. Sasuke defeats them all, but declares that he wants to kill Itachi more than them. Naruto continues his training by summoning Gamakichi and Gamatatsu, but still doesn't understand the concept of connecting to another person's heart. Kabuto and Yūkimaru arrive at the Hot Springs Village where Naruto and Jiraiya are.

Guren is rendered unconscious and relives her past as Naruto is caught in an illusion about Sasuke. After Kakashi finds him, Teams Kakashi and Kurenai conclude the mist around them causes Genjutsu courtesy of the Three-Tails. After Guren wakes up, Yūkimaru suffers another fever and passes out. Tsunade hears of the Three-Tails and assmbles Shizune, Ino, Tenten and Lee to go and seal it before the Akatsuki do. Naruto and Sakura talk about the home that people should return to before Naruto heads off to find Yūkimaru.

Sasuke's Sharingan proves to be superior against Deidara's explosives. Deidara creates one of his finest works, the C4 Karura, in order to take him down. What will Sasuke do now?

Jiraiya is now confronted by two new Pains who both possess different abilities than the one he was fighting. Just who is Pain and how many Pains are there?

The code Jiraiya left behind is finally deciphered, but what exactly does it mean? Meanwhile, Naruto continues his training.

Ebisu protects Konohamaru from Pain and refuses to divulge any information about Naruto. Ebisu is willing to give up his life in order to protect both Naruto and Konohamaru. Konohamaru isn't about to let his teacher throw his life away, but what can he possibly do against Pain?

Sakura reflects upon a time when she was infected with a strange disease by Naruto. In order to find a cure, an order was issued for Naruto to be quarantined at all costs before he could infect anybody else.

Might Guy recalls their "visualization" training with Lee in order to avoid learning the Drunken Fist and forgetting an incident which Might Guy apologizes to the restaurant owner with humiliation. Lee, who is determined to train to be stronger than Naruto, follows Might Guy's orders and resemble animal fighting styles which represent on a restaurant menu. However they failed, until they tried on training on a moving boat. Like Guy who has seasickness, Lee also suffers from seasickness but he uses it to balance the boat which resembles exactly as the Drunken Fist fighting style. Guy lately realizes that Lee is also aware of the restaurant incident and Lee was only protecting Guy from a drunk man which causes the restaurant to be totally damaged.

Tenten remembers when she was little and how she really wanted to become like the legendary Tsunade. She finds out through hard training that she won't be capable of the strength Tsunade has. She also finds out that she won't be suitable to be a medical ninja for her poor chakra control. But at last, she discovers that she has the ability to summon ninja tools, thus creating her own style of fighting.

Sixteen years ago, Fourth Hokage Minato Namikaze and his wife Kushina are expecting their first child, much to the delight of the young couple.

As Darui and his First Company engage an army of White Zetsu, the remaining forces must deal with reanimated shinobi.

Kankuro’s Commando Unit is cornered by Hanzo’s poison attack. Fortunately, Mifune and his Fifth Company arrive in time to provide assistance.

While training in Chakra Mode, Naruto senses the presence of the Nine Tails’ chakra seeping from Kinkaku outside. Curious to find out what’s happening, Naruto tries to leave the training room when Iruka suddenly steps in to stop him.

Over at the Medical Unit camp, Sakura and the other medic ninja work nonstop to treat the wounded. Neji is there to recover from overusing his Byakugan.

Tsunade and the Raikage arrive to prevent Naruto and Killer Bee from joining the battle. But the two Kage fail to convince the Jinchuriki to turn back, forcing the Raikage to use extreme force.

Gaara leads the Fourth Company into battle against the previous Kage, including his father, the late Fourth Kazekage. The Fourth Kazekage attacks Gaara in order to determine if his son is truly worthy to be the current Kazekage.

Naruto and the others finally regain their lost memories regarding Yota. Years ago, the Leaf Village kids came to befriend Yota, but the adults believed the young boy was a spy and took him away for questioning.

Naruto and Killer Bee take on the six Reanimated Jinchuriki, who’ve been equipped with the Rinnegan. Using his past experience from fighting the Six Paths of Pain, Naruto devises a plan to stop the Jinchuriki.

Kabuto attempts to bring Sasuke over to his side by pointing out that they both are fighting for the same goal: to bring down the Leaf Village. But Sasuke quickly rejects him.

Thanks to Itachi, the Reanimation Jutsu is released, and all the Reanimated Shinobi are returned to their resting places. But to everyone’s surprise, the real Madara still remains!

Obito watches in disbelief as Kakashi kills Rin. Unable to accept the harsh reality, Obito decides to carry out Madara’s dream so that he can create an ideal world where Rin still exists.

Orochimaru is forced to flee the Hidden Leaf after Third Hokage Hiruzen exposes his illegal experiments. Danzo, fearing that Orochimaru’s capture would lead to the exposure of his own involvement in the experiments, sends out one of his men to help.

Itachi Uchiha is inducted into Kakashi’s unit as the youngest member of the ANBU Black Ops. Itachi’s father, Fugaku, is pleased, thinking this will grant the Uchiha access to exclusive, top-secret Leaf intel.

Kakashi desperately tries to reach out to Obito, but his words fall on deaf ears. Obito instead accuses Kakashi of being trash, which angers Naruto, forcing him to step in and defend his Sensei.

The Senju and Uchiha clans join together to build a shinobi village and fulfill their dreams.

Team 7 is finally reunited when Naruto, Sakura and Sasuke join forces.

The Ten Tails morphs into its final form, "The Divine Tree," and attacks the shinobi, absorbing their chakra one after another.

All the Tailed Beasts are freed, and old friends Kakashi and Obito come face to face with each other. What will Obito's response be? Meanwhile, the Tailed Beasts and the Allied Shinobi Forces shift their focus onto their greatest foe, Madara Uchiha. Gaara is reunited with his former Tailed Beast, Shukaku. When Gaara asks Shukaku to lend his power to seal Madara, he refuses. Will their history of animosity prevent them from working together?

When Hinata is labeled unfit as a successor, Hanabi's heart becomes bound to her destiny.

Neji and the team come across Matsuri collapsed in the desert and find out that Gaara is in danger. Meanwhile, the chains of a mysterious priest bind Gaara and Foo.

It’s been three years since Naruto set out to train with Jiraiya, and he's just returned to the Hidden Leaf Village. Konohamaru immediately begs Naruto to teach him a new jutsu and he starts to go over the basics...but his explanations are very vague. Soon after, Naruto sets out on a mission, leaving Konohamaru to figure it out alone!

Tenten falls under the Infinite Tsukuyomi and wakes up in the Hidden Leaf Village. When Lee and Guy Sensei appear, Tenten is relieved to see that she is not alone. But her joy is short-lived, as both men act oddly and are dressed stylishly—just where has she been transported to?

Tsunade continues to read Jiraiya’s novel. Chunin- and jonin-level ninja have gone missing, and the Fourth Hokage, Minato, orders a search mission with teams of genin led by Guy and Kurenai. Kakashi’s Team 7 is also dispatched, but the hero Naruto Uzumaki, despite being the Hokage’s son, has the misfortune of being labeled a loser.

Sasuke has left with Orochimaru, but Naruto is not about to give up. Determined to bring Sasuke back, he returns to the village with Shikamaru and the others. Meanwhile, Yahiko appears in the village, calling himself “Pain" and seeking revenge for the Hidden Leaf’s betrayal.

Seeing Hinata almost die triggers Naruto’s anger and he goes into Nine Tails State. Naruto's power is enormous, but Pain releases his jutsu to seal him away. Hatred consumes Naruto as he tries to break the seal. With Naruto unable to calmly control the Nine Tails’ power, the village steadily heads toward destruction.

Itachi becomes a rogue ninja and joins the Akatsuki. He is welcomed and introduced by Pain and Orochimaru as the ex-Leaf ANBU and the man who massacred his entire clan. Itachi is paired up with a man named Juzo, and their first job together is to fulfill an assassination request in the Land of Water.

The Infinite Tsukuyomi does not affect Hashirama, Tobirama, Hiruzen and Minato because they are reanimated. Hagoromo, the Sage of the Six Paths, appears and explains to the four that Hashirama and Madara are the reincarnations of his sons Ashura and Indra. Hagoromo recounts the tale of how he founded Ninshu, the Ninja Creed, and about the lives of Ashura and Indra.

Chakra—whose energy connects this world to those beyond—allows Obito to leave Rin's side for a moment and appear in Kakashi’s inner psyche. Obito gives him his Magekyo Sharingan and leaves with a parting wish that Kakashi become the Sixth Hokage.