Naruto's been having nightmares about the release of the Nine-Tail's power. Afterward, Kakashi informs Naruto that he has special training for him that will make him strong quickly. They are cut off by Team 10, who have also come to visit. Sai lunches with them and, trying to make friends by using nicknames, angers Sakura by calling Ino "gorgeous" after concluding that women do not like to hear how they really are.

Kakashi is released from the hospital and begins Naruto's training program. Naruto learns that he has Wind-style chakra. Yamato helps by setting up the training field with his special jutsu. Naruto also learns that he can use his Multi Shadow Clone jutsu to speed up his training, since whatever the clones learn, the original user learns upon the clone's dispersal. Naruto and his mass of clones each take a leaf and attempt to slice it in half with wind chakra as the first step to creating his new jutsu.

Naruto and his clones continue to work on chakra nature manipulation by slicing leaves. After some struggling, Naruto approaches Asuma, who is also a wind type, for advice, after which Asuma gives Naruto's clone a few pointers. Naruto is subsequently able to slice a leaf in half. Asuma and Yamato head out with their teams on new missions. It is revealed that Asuma is the Third Hokage's son and that he is in a relationship with Kurenai. Meanwhile, on a hill overlooking a burnt village, four cloaked figures discuss the awakening of the Fire Country by eliminating the Leaf Village.

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.

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.

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.

Team Kakashi begins facing off against the enemy shinobi. Yamato eludes his opponent, Fudo, by faking his death. Sora, unwilling to look for Naruto, goes off on his own. Back in Konoha, Danzo reveals that he is aware that he is being watched by Tsunade's ANBU. Naruto fights Fūka, whose kiss is fatal and shows her ability to use earth, fire, water and lightning jutsus. Sai manages to escape from his attacker, Fuen, and later saves Sakura from an enormous spider, becoming injured in the process. Sora then hits upon the enemy leader, Furido, and it is revealed that he was the group's target.

Furido taunts Sora until Sora unleashes his true powers, before informing Sora that he is planning to use the four corpses to save the Land of Fire. Naruto continues his fight with F?ka and learns that she can use all five elements. F?ka manages to kiss Naruto and begins draining his chakra. Realizing that Naruto is in trouble from extra-sensory perception, Sora rushes to rescue him. Sakura, Sai and Yamato arrive to help but are trapped by Fudo and Fuen. F?ka drains Naruto's chakra until she begins drawing on the Nine-tails's, which is too unnatural for her to successfully absorb. The enemy team retreats when Chiriku brings reinforcements.

Asuma's team returns from its mission. Team Kakashi returns to Konoha as well, with Sora replacing Sai on the team. Naruto tries to show Sora around Konoha but Sora goes his own way. Sora's insults precipitate a brawl with Kiba and Choji, with Naruto and Rock Lee joining in. Shikamaru and Asuma stop the fight. Later Asuma tells Sora he knew Sora's father, who is revealed as one of the Guardians involved in the coup attempt. He also shows Sora his chakra blade attack. Furido and the other body snatchers begin their attack on the Kohaku Clan.

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.

Danzou is brought in for questioning after being caught meeting with a young Rain ninja. Sora confronts Asuma, and Asuma admits to having killed Kazuma. He attacks Asuma, his arm once again assuming a demonic form. Afterward, Naruto gets injured while shielding Sora from the attacks of an unknown individual, presumably from Root. Furido then approaches Sora, telling him to kill both Asuma and the Hokage to avenge his father. Later on, Naruto catches Sora going after Tsunade. Sora retreats as Shizune and a few other ninja arrive, but Naruto pursues him. At that moment, a mysterious lightning storm strikes, cutting off power to the entire village.

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.

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.

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.

Naruto deduces that Fuuka's secret consists of switching bodies to use each corresponding element and that her hair preserves her youth and body. Naruto damages her hair and it takes a life of its own dispensing the body, but Naruto finally kills it with a Rasengan. Meanwhile, Asuma manages to break free of the electric barrier, catch up with Kitane and defeat him in a short fight. Realizing that Kitane is no more, and that his three other companions were killed, Furido causes the 3 other ninja guardians to disappear. But Furido has a back up plan, Sora.

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.

The chakra of the Nine-tails rages out of control within Sora, preventing Naruto and the others from subduing him. Asuma and Kazuma resume their old battle, while Kazuma justifies his actions with his duty as a pawn to the "King" of the Fire Country. Naruto is repeatedly knocked down in his attempts to restrain Sora, and the chakra seeps into him and transforms him as well. Yamato is unable to suppress the Nine-tails' chakra in both Jinchūriki, being prevented by an unknown outside force. Sora's fourth tail emerges, causing the Nine-tails's Cloak to envelop his body. He temporarily gains his own consciousness when he witnesses Naruto stab himself in the leg and successfully prevent the original Nine-tails' Cloak from emerging.

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.

In the aftermath of the destruction of the Leaf Village, Iruka thinks back to the time when the Third Hokage first gave him the task of being Naruto's homeroom teacher at the Academy, since no one else would take him in.

Iruka struggles to deal with his hate for the Nine-Tailed Fox inside Naruto as he tries to connect with Naruto after seeing him shunned by his peers.

After discovering a kunai knife with a secret message on it, Naruto winds up being pursued by three kunoichi from the Hidden Waterfall Village. Iruka mangaes to find him, but when the situation grows worse, Kakashi appears to save them both.

Kakashi has a flashback back when he was assigned to be the sensei of Team 7. In a bid to know his students, Naruto, Sasuke & Sakura, better, Kakashi spies on them and to see how they would all get along as a group. Angered by Sakura's talk about calling Naruto a brat and that he has no family to tell him right or wrong, Sasuke tells Sakura she is annoying. Realizing Sakura's sadness, Naruto goes to battle Sasuke, but gets defeated. It then goes back to the present and Kakashi claims that it is up to him to stop Sasuke.

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.

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.

After hearing the news about Akatsuki's attack on the Hidden Leaf Village, Gaara worries about Naruto's well-being. He remembers a time in the past where Team 7 was assigned to help him out with a problem, and how nobody, especially Naruto, was eager to trust him. Yet, when his life was put in danger by people he had wronged, Naruto was the first to come to his rescue.

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.

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.

An ostrich tells a story of when Naruto, Rock Lee, and Shino, all led by Kotetsu, entered the Leaf Village's animal district in an effort to find and subdue him. However, he and the other animals proved that they weren't willing to go down without a fight.

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.

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.

After having discovered that the village was under the control of rebels from the Hidden Rain Village, led by Hanzo, Naruto and Jiraiya decided to take action to help save the women and children taken hostage and free the village from the Rain's tyrannical control.

In the past, Naruto and Sakura joined Sasuke on a mission to collect the paw print of Nekomata, a large and powerful two-tailed ninja cat that ruled over all of the ninja cats.

Naruto, two jonin and an elder known as "the Eternal Genin" set off to a mission to patrol the border of the Land of Fire following Orochimaru's attack. After some days with no incidents, a group of enemy ninjas cross the borders. The Eternal Genin proves to be a brave ninja and remembering the lessons he learned with the 2nd and 3rd hokages, sees the similarities between Naruto and his father.

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.

Konohamaru's team asks Neji to talk about Naruto's heroism. Instead, Neji tells them about an incident during the Chunin exams three years prior. While Orochimaru attacked Konoha, two rogue ninja take advantage of the commotion and kidnap Hinata. Neji, Tenten, Kiba, and Akamaru rush out to save her. They're in trouble until Hiashi shows up and saves them, telling Neji that he's the beloved memory of Hiashi's younger brother. Neji realizes Naruto's speech about destiny was right; he isn't just a slave to the clan name. Konohamaru's team complains that Naruto wasn't in the story at all, and Neji cryptically answers that Naruto was the most important part.

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?

Naruto thinks back to the time when Team 7 was on a mission to capture a group of thieves who stole a golden statue. When making a move on the thieves, Naruto and Sasuke had managed to take back the statue but were separated from Sakura, who was captured. On top of that, the thieves' leader had used a special thread-like technique to bind one of Naruto's hands to one of Sasuke's. Literally stuck to each other, would Naruto and Sasuke be able to work together to save Sakura and keep the golden statue safe at the same time?

Shikamaru remembers the time when Teams 7 and 10 joined together to flush out a band of bandits who were terrorizing a nearby village and had kidnapped the headman's granddaughter. With no assistance available from Kakashi or Asuma, Shikamaru was forced to lead the team of genin to the bandits' fort and come up with a plan to rescue the headman's granddaughter.

Sasuke has a flashback while traveling to Konoha with his team, Taka. He once saved a girl named Naho not knowing that she's a relative of the Feudal Lord. Meanwhile, Naruto and Sakura are sent on a mission to accompany Naho and act as her bodyguards while Kakashi and Sasuke are sent to discover the reason why internationally wanted bandits have entered their border. Kakashi and Sasuke later find out that the bandits intend to abduct Naho. Naruto and Sakura are defeated by the bandits and are taken hostage. Sasuke finds them first and proceeds to defeat the leader and mercilessly punches him because of his jealousy for Naruto's growing power. A cut to the present reveals Naruto contemplating on his promise to have Sasuke return to the village.

Naruto makes his entrance onto the battlefield and uses his sensory powers to detect and destroy the transformed White Zetsu clones. During the battle, Shikaku updates Naruto with what they currently know on Madara.

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 Killer Bee engage in battle against the reanimated Itachi Uchiha and Nagato. Itachi learns from Naruto that Sasuke has chosen the path of vengeance.

Itachi uses the ultimate genjutsu technique Koto Amatsukami to free himself from the Reanimation Jutsu. Itachi then joins Naruto and Killer Bee to fight Nagato, who is still under Kabuto’s control.

The Fourth Company continue their fight against the reanimated Kage. Gaara and Ohnoki team up to hold off Second Tsuchikage Mu, while the remaining shinobi take on the Second Mizukage, who is willing to be sealed away.

Temari leads the attack on the Third Raikage using Wind Style, but even her strongest jutsu is not enough to penetrate the Raikage’s invincible armor.

Gaara and Ohnoki manage to overcome the Second Mizukage’s mirage attack. Having taken an interest in Gaara, the Second Mizukage decides to further test the young Kage’s skills.

Shikamaru, Choji, Neji, and Kiba find themselves up against some familiar faces from the past. The Sound Ninja Four have been brought back by Kabuto’s Reanimation Jutsu, and they are ready to seek vengeance.

Shikamaru, Neji, Choji, and Kiba succeed in defeating the Sound Ninja Four. But the enemy uses the Underworld Transfer Jutsu to trap the Leaf shinobi’s souls inside a barrier.

Time is running out for the Leaf shinobi whose souls are trapped inside the Sound Four’s barrier. Ino and Shino exhaust their own chakra to keep their friends alive.

Hinata defends Neji from a White Zetsu clone while he’s recovering from an earlier fight. She then remembers the time Neji protected her the same way after she temporarily lost her sight.

Three years ago, Leaf Anbu Yugao Uzuki lost her lover Hayate Gekko in battle. Unable to cope with his death, Yugao has since left the Anbu and joined the Medical Corps. Meanwhile, Kabuto has reanimated Hayate.

Yugao is ordered by Sukui to track down the reanimated Hayate. Still shaken by her lover’s unexpected return as an enemy, Yugao manages to catch up to Hayate and his men.

Naruto arrives to help a team of Allied Shinobi Forces led by Karui, who are struggling against a reanimated samurai. Naruto recognizes the samurai as Tatewaki, a man he met during a past mission.

The Leaf Shinobi succeed in bringing young lord Shu into custody, placing a disguised Naruto as his double. But Tatewaki soon uncovers Naruto’s identity and surrounds the intruder with his men.

Madara is prepping his new jutsu Limited Tsukuyomi, choosing Naruto as his test subject. Meanwhile, Naruto is spending his day off alone in his room. Thinking that Naruto is lonely, Lee suggests they all go to the bathhouse for some relaxation.

Might Guy arrives on the battlefield to stop a Reanimated Shinobi who he recognizes as Master Chen, the legendary Taijutsu User from the Third Great Ninja War.

A reanimated boy who can control weather appears before Team Ino-Shika-Cho, Sakura, and Kiba, who are all fighting in different locations. To their surprise, the boy seems to know them.

The weather-controlling enemy is revealed to be Yota, a boy who came to the Leaf Village years ago and befriended the local kids, including Naruto.

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.

Kabuto reanimates an army of unknown shinobi led by Danzo’s former bodyguard Torune to retrieve the ones he lost to the Allied Forces. But aside from Torune, the reanimated shinobi are all weak and are quickly sealed away.

During their battle against the White Zetsu, Shino’s beetles detect the presence of another enemy. Leaving the fight to Kiba and the others, Shino goes to investigate and finds Torune preparing to unleash his forbidden jutsu.

Kabuto reanimates Fukai to attack Killer Bee and Motoi. Fukai warns Killer Bee to escape before being taken over by Kabuto. To everyone’s surprise, Fukai releases Eight Tails’ chakra and enters Tailed Beast State.

A reanimated Granny Chiyo attacks Kankuro and Mifune’s team. Kankuro fights back by using the human puppet of Sasori. The sight of Sasori causes Granny Chiyo to recall the painful memories that led her grandson to create his human puppets.

The Allied Forces receive a report that Omoi has deserted his post, much to the Raikage’s shock. It is soon revealed that Omoi has defied orders to go save the Thundercloud Unit.