An older and stronger Naruto returns from his two and a half years of training with Jiraiya. When he gets back he finds that many things have changed since he left. From Konohamaru becoming a Gennin and being under the supervision of Ebisu to Tsunade's, the Fifth Hokage, being added to the great stone faces. Now the tasks of starting things where they were left has begun. And what new danger does Jiraiya know about?

As Naruto gets back into the swing of things and meets back up with what is left of Team 7, Kakashi and Sakura, Jiraiya has something important to tell them. It seems a shinobi group known as Akatsuki is on the move. The things they are after are the tailed beasts like the one inside of Naruto, the Kyubi. Is Naruto prepared to defend himself from this group of Shinobi?

The bell test begins again while Tsunade, Jiraiya, and Shizune watch, but this time Kakashi is taking things seriously. So serious that he is using his Sharingan. Can Naruto and Sakura get the bells before the deadline? Meanwhile Gaara searches for the Akatsuki member that has invaded the village.

The bell test continues for Naruto and Sakura. Meanwhile Gaara discovers that the Akatsuki member, Deidara, has infiltrated the village. Now the battle begins between Gaara and Deidara. With Deidara after Shukaku which is sealed in Gaara, can the older and more powerful Gaara defeat this powerful foe?

Gaara and Deidara continue their fight with Gaara gaining the upper hand. Deidara then begins to attack the village and Gaara, the Kazekage, must protect it. Can Gaara defeat Deidara or is he playing right into his hands.

Deidara launches an attack on the village and Gaara must do his duty as Kazekage and protect it. However, Gaara's left himself wide open for an attack!

With Gaara captured and abducted, Kankuro goes after Deidara to get him back. However, his path is soon blocked by Sasori, whom doesn't plan on letting him pass.

With their leader abducted, the Hidden Sand Village requests assistance from Konoha. Tsunade sends Naruto, Sakura, and Kakashi out to help. Worried about her little brother, Temari tags along as well.

As the group travels to Hidden Sand Village, Naruto realizes that Sakura doesn't know why Akatsuki are after Gaara and himself. Has the time finally come to tell her the truth?

With Kankuro injured, Chiyo and Ebizou make an appearance in order to save his life. They try everything, but it's all in vain and Kankuro's condition is progressively getting worse. Meanwhile, Sasori and Deidara arrive at the Akatsuki hideout and begin extracting Shukaku from Gaara using a mysterious technique.

Upon arriving at the Sand Village's medical center, Kakashi is attacked by an elderly woman. Who is this woman and why is she attacking Kakashi? Meanwhile, Sakura does an examination on Kankuro and figures out that he's in bad shape. Can she use what Tsunade taught her in order to save Kankuro's life?

When Pakkun discovers the whereabouts of the Akatsuki's hideout, Kakashi orders Pakkun to find Gai and his team and lead them to the position. Meanwhile, Kakashi and his group decide to head out with Temari and other sand ninjas, but Chiyo decides to go in her place. Will this old woman help or hinder the mission?

While Gai's group must fight against Kisame in order to proceed, Kakashi's group is cut off by another familiar face...Itachi Uchiha! Kakashi and Naruto team up and face the legendary ninja, but will even that be enough?

While Gai, Lee, Tenten and Neji continue their battle against Kisame, Naruto and Kakashi work together to fight Itachi. But when Itachi puts Naruto in a genjutsu spell, can Naruto find a way to break free?

The fights against Itachi and Kisame finally come to an end, but are these the real Itachi and Kisame?

As the group draws closer to Akatsuki's hideout, Chiyo reveals some startling information about the Jinchuuriki. Naruto becomes more determined than ever to rescue Gaara, but is it too late to save him?

The group has finally arrived at the Akatsuki hideout, but is it already too late to save Gaara?

Knowing that Akatsuki's lair is protected by a powerful barrier, Kakashi and Gai decide that the teams must work together to dismantle the barrier.

As Gai's team stays behind to fight a group of mysterious enemies, Kakashi's team enters the Akatsuki hideout, where Naruto makes an unhappy discovery.

Chiyo and Sakura team up to fight Sasori, but soon realize that if they get something even as small as scratch, it's all over. Can the two defeat this puppet master?

With his puppet destroyed, Sasori reveals himself to Chiyo and Sakura, looking no older than when he left his village twenty years ago. As a further bit of nostalgia, he produces a summoning scroll and calls forth the Third Kazekage, whom Sasori has made into a puppet. Using its weapons, which are even more dangerous than Hiruko's, Sasori is able to catch Sakura in a poison gas cloud. Meanwhile, Kankuro, Temari's team, and Ebizo make their way to the Akatsuki hideout.

Sakura manages to escape the poison gas cloud by using an explosive scroll on herself. Chiyo calls forth the "Mother" and "Father" puppets that Sasori created to fight him and the Third. They manage to hold down the Third for awhile until Sasori releases the Third's secret technique: Iron Sand. Meanwhile, Team Guy are having trouble fighting the clones and showing exhaustion from the battle. Naruto and Kakashi manage to avoid Deidara's clay bombs and keep up with him.

The Iron Sand stops both puppets from moving. Chiyo's right arm (which she had turned into a puppet) gets clogged and broken as well. Chiyo thinks back to the past and remembers how Sasori created and controled his first puppets, Father and Mother. Sakura urges Chiyo to use her again as her puppet. With Chiyo's help, Sakura avoids the columns formed by the Iron Sand to attack her.

Chiyo and Sakura must try and defeat Sasori's strongest puppet, the Third Kazekage.

Sakura has managed to destroy Sasori's strongest puppet, but he still has a few tricks up sleeve. And although Sakura's managed to avoid a fatal blow from the poison, she and Chiyo must defeat him in three minutes before the antidote wears off and they are vulnerable to Sasori's attacks. Can they defeat him in time?

Chiyo uses her abilities as a master puppeteer to allow her to control ten puppets at once against Sasori. However, Sasori has gone a step ahead, and gained the ability to control one hundred puppets at once! Can Chiyo defeat the man who took down an entire country?

It's the final stand against Sasori, and Chiyo reveals the flaw in Sasori's "immortality". As Sasori breathes his last breaths, he rewards the two kunoichi for his defeat by providing them some valuable information. In ten days, they will have the opportunity to meet with one of his spies who can provide them with information on Orochimaru, and Sasuke as well.

As Kakashi and Naruto chase after Deidara, and Sakura and Chiyo rest from their fight with Sasori, Gai and his team continue to fight their doppelgangers. Things aren't looking good for the four as the doppelgangers remain at the same strength while Gai's team grows weaker. Can they finish things up, or will it be the end of the line for them?

Kakashi unleashes his new Mangekyo Sharingan against Deidara, turning the tide of the battle in their favor, but when Naruto begins to act strangely, Kakashi sees him as the bigger threat.

Kakashi must act quickly to calm Naruto down before he releases too much of Kyubi's power. Meanwhile, Deidara is cornered by Gai's team, and when he realizes that he can't defeat them, he decides that the only way he'll die is he takes everyone else with him!

Gaara's body has finally been recovered, and Chiyo determines that there is only one way to save him. It's up to her and the entire village to prove to Gaara that he is loved, and Naruto shows Gaara that he does have a friend.

Now that Gaara's been revived, the Hidden Sand Village slowly begins to return to normal. It's time for the ninja of Konoha to take their leave, and Naruto shows Gaara how friends say goodbye. Meanwhile, a mysterious ninja tries to join Akatsuki.

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, Choji and Shikamaru attempt to capture and interrogate Sai, but Sai withdraws after insulting Naruto. Shortly afterward, Ino appears. Concerned that the demon fox could fall into Akatsuki hands, the village elders challenge Tsunade's plan to send Naruto out of the village without the still bedridden Kakashi. Tsunade promises to protect Konoha with her own life if Naruto is captured, but is still forced to compromise with Danzo by adding Sai to Team Kakashi. She also temporarily replaces Kakashi with ANBU member Yamato and warns him to keep an eye on Sai. Naruto and Sakura finally meet their new team members, and Naruto is immediately angered upon Sai's appearance.

Yamato takes temporary leadership of Team Kakashi while Sai insults both Naruto and Sakura. While preparing to set off, Sai receives an envelope from a Root shinobi containing secret orders from Danzo, and Sakura consults with Tsunade. Jiraiya then meets with Tsunade and Yamato in Kakashi's hospital room to brief Yamato on the demon fox within Naruto, detailing the "demon fox's cloak", and revealing a scar he got from Naruto when the fourth tail formed. Finally the new Team Kakashi set off on their new mission, to intercept an Akatsuki spy and gather information about Sasuke.

The new team Kakashi heads out for the Heaven and Earth bridge. Sai, Sakura, and Naruto come to blows after just 5 minutes on the same team due to Sai making fun of Sasuke. Therefore, Yamato decides they need to improve on teamwork and uses Mokuton to create a wooden cage threatening to lock the team up unless they behave. Given an ultimatum between being locked up or spending the night at a hot springs, the team chooses to visit the springs to improve team cohesion. Naruto still despises Sai despite this effort, and several insulting remarks from Sai worsen team relations.

Sakura sees Sai drawing by the river and finds out that Sai has artistic talent but has never given titles to anything he ever drew. Naruto and Sakura begin to realize the reason behind Sai's repulsive personality. After the hot springs, the team heads off to the bridge to meet the spy. Yamato is suspicious of traps so they go off the main road into the forest. Camping for the night, Yamato then creates a two story house by again using his Mokuton jutsu. Inside this house, the team formulates their plan.

Naruto is paired with Sai for the Buddy team of two, over his and Sakura's objections, while Sakura is assigned to support Yamato. Yamato conducts a simulation of the spy meeting with himself as the spy to gauge Naruto and Sai's abilities and teamwork. After Naruto makes a mistake when attacking Yamato, Sai immobilizes him and goes on to capture Yamato alone. Naruto is angry with Sai for not acting as a comrade would, but resolves to work together with him if doing so will help bring Sasuke back. Sai reveals to Sakura that he has no emotions, and little understanding of them. The group then prepares to head to the bridge.

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.

Immediately after Yamato signals Naruto and the others out to the bridge where Orochimaru and Kabuto are waiting, Naruto's chakra begins to boil with the chakra of the Nine-Tailed Fox. Slowly, Naruto grows more tails as Orochimaru taunts him and makes him even more angry. Meanwhile, Yamato remembers Jiraiya speaking of how many tails he has seen Naruto grow. Jiraiya explains more about what happened and more about how Naruto acts when he's in his Nine-Tails form.

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.

Naruto, in the four-tailed state, begins attacking Orochimaru with incredible force, devastating the surrounding landscape and preventing Sai and Yamato's wood clone from approaching him. The majority of Orochimaru's attacks prove to be ineffective, but Naruto also fails to kill Orochimaru as he regenerates from any injuries he sustains. Meanwhile, Kabuto advances toward Sakura and Yamato, deducing that Sasori has died. Orochimaru finally manages to strike Naruto with a sword blade from his mouth, and Sakura reacts in horror when she sees Naruto's four-tailed state.

Kabuto comments that Naruto's state is a consequence of his desperation to bring back Sasuke. Sakura begins to cry and approaches Naruto but is injured when his attention turns to her. Yamato uses the mokuton jutsu to bind Naruto before he does any more harm. Kabuto heals Sakura, reasoning that the Konoha ninja are not Orochimaru's enemies because they are also fighting Akatsuki. Yamato uses the abilities of the 1st Hokage to forcibly return Naruto to his normal state. Meanwhile Sai confronts Orochimaru with a message from Danzo. Orochimaru responds by piercing Sai with Kusanagi.

Yamato uses the first Hokage's chakra to suppress the demon fox's chakra and Naruto returns to normal, but with severe injuries. Sakura begins to heal him, but notes that medical ninjutsu has little effect on his wounds. Orochimaru's sword is revealed to have only pierced one of Sai's clones. The real Sai emerges, talks to Orochimaru and gives him a letter from Danzo. Sai then leaves with Orochimaru and Kabuto but Yamato's wood clone stays close on their trail. Naruto comes to his senses and wonders what happened but Sakura decides not to tell him the truth. They reach the meeting spot, picking up the picture book Sai left behind. Yamato infers that Danzo seeks to destroy and remake Konoha by collaborating with Orochimaru.

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.

Naruto finally makes sense of the destruction he witnessed around him earlier. Yamato tells Naruto not to rely on the demon because Naruto is strong enough to withstand the demon's terrible chakra. Sai discovers the loss of his book while resting. Team Kakashi browse Sai's book, and they notice that the book (which can be read from both ends) contains different paths of two boys who meet in the middle. Each page has the boys fighting someone new, each time collecting the opponent's armor and weapons into the next page. The pages where the two boys would meet are unfinished. Orochimaru's group reach their base, not realizing that Yamato's wood clone trailed them there. Sai gets a glimpse of Sasuke's silhouette and eyes and discovers that he is the man Naruto and Sakura are looking for.

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.

Yamato and the team enter Sai's room and confront him while Kabuto makes his way there as well. Sai tells Team Kakashi that not only was he to help with Konoha's destruction but also act as a spy against Orochimaru. Yamato reveals the secret of "Root"- its members were trained like Kirigakure's students in that they had to kill their friends so as to eliminate their emotions. Sakura returns Sai's book to him, remarking that he still has emotions because he treasures it. Sai then tells the group about his bond with his brother. Finally the team decides what to do about Sai's betrayal outside the lair. In doing so, Naruto tells the group about his own bonds and about how far he's willing to go to bring Sasuke back.

Kabuto fights Team Kakashi and frees Sai. However, Sai, who intends to learn more about his bond with his brother through Naruto's bond with Sasuke, betrays him. Captured, Kabuto gives a vague description of Sasuke's location to the team. Leaving Yamato's wood clone to watch over Kabuto, Team Kakashi enters Orochimaru's hideout and splits up to find Sasuke.

As Team Kakashi continues their search for Sasuke, Naruto suddenly collapses due to his previous fight with Orochimaru. As Naruto wakes up, Sai begins to reveal more about his brother, but Orochimaru suddenly attacks them. Sakura and Yamato come to Naruto's aid against Orochimaru, while Sai continues the search. Just as Sai finds Sasuke, Yamato finds Sai's bingo book with Sasuke listed as a target for assassination.

As Team Kakashi continues their search for Sasuke, Sai approaches Sasuke's room and awakens him. Shaken by the image of Sasuke's Sharingan from earlier, Sai attempts to restrain him. A large explosion occurs and Sakura, Naruto and Yamato catch up. At first Sakura tries to restrain Sai in order to find out his true objective, but she stops, stunned at seeing her former comrade. Contrary to what the rest of the team assumed to be his mission, Sai tells them that he wishes to bring Sasuke back to Konoha.

Sasuke begins to attack Naruto, but Sai restrains him only for them both to be blown away by Sasuke's Chidori Nagashi. Sakura charges at Sasuke, but Yamato intervenes and winds up being stabbed by Sasuke's unique blade infused with his Chidori. The Nine-Tailed Fox tempts Naruto with its power, but he refuses it. Sasuke sees this using his Sharingan, appearing in Naruto's mind. The Nine-Tails says that Sasuke's chakra reminds him of Madara Uchiha, then Sasuke suppresses the Nine-Tailed Fox's chakra. Before the Nine-Tailed Fox returns to its cage, it warns Sasuke not to kill Naruto, saying that he will live to regret it forever.

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'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. 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.

Asuma apologizes at the grave of the Third Hokage for not understanding his advice concerning what the "king" of the Fire Country is. At the hospital, Naruto and Sai recover, despite Naruto's desire to resume his training. Tsunade receives a report from Kakashi that Akatsuki is on the move. Elsewhere, Yugito Nii, the Two Tails Jinchūriki, struggles against Hidan and Kakuzu and unleashes the Two Tails, but is defeated and captured. Hidan and Kakuzu then turn their attention to the Fire Country for their next target.

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.

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.

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. It is also revealed that Kakashi can perform the Rasengan.

Kakashi reveals that while he knows how to perform Rasengan, he cannot combine his own lightning-based chakra. He adds that even the Fourth Hokage, who created the move, could not combine his elemental chakra with the technique, but that Naruto might be able to. Asuma sends word to other teams about Akatsuki’s location and proceeds on despite his concern about Akatsuki’s strength. Kakuzu turns in Chiriku’s corpse despite Hidan’s complaints, and says that he is partnered with Hidan because he cannot kill him. The stress of the training causes Naruto to be enveloped in the Nine-tails's "Demon Fox's Cloak", but Yamato suppresses it.

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.

Asuma’s fire jutsu strikes Hidan, but much to the team's surprise, Asuma is also burned. Hidan reveals his ability: By ingesting an opponent’s blood and standing in a ritual circle drawn with blood, the "curse" links him to his opponent and all damage inflicted on him is also inflicted on the opponent. Asuma rushes at Hidan but collapses after Hidan stabs himself in the leg. Shikamaru realizes Hidan needs to be in the circle for the curse to take effect, and uses his shadow possession jutsu to force Hidan to step out of it. Asuma forces himself to stand up and beheads the restrained Hidan.

Hidan’s immortality enables him to stay alive even with his head cut off, although he cannot move his body. Kakuzu sews Hidan's head back on with threads that sprout from his body. Izumo and Kotetsu try to attack Kakuzu, but he manages to grab them both by using his body threads, restraining them and suffocating them as well. Hidan, now able to move again, returns to the circle and stabs himself with the blades of his scythe; he finishes it off by stabbing himself in the chest with another spike, fatally wounding Asuma.

A call from the Akatsuki leader forces Hidan and Kakuzu to fall back, but in the wake of the aftermath, not everyone makes it back to Konoha alive.

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.

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

When Kakashi strikes Kakuzu through the heart, the battle seems to be over. However, when Kakuzu not only survives the attack, but also manages to escape from Shikamaru's trap, it soon becomes clear that the fight is only just beginning..

As Kakashi and the others continue to struggle against the Akatsuki duo, Kakuzu reveals that he has not one, but five hearts! In order to kill him, one must take out all five of his hearts. Meanwhile, Shikamaru decides to challenge Hidan alone, and forces him away from his partner.

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.

Hidan falls into Shikamaru's trap, but now that he has Hidan cornered, can he find a way to defeat Hidan's immortality? Elsewhere, things are looking grim for Kakashi, Choji, and Ino as they continue fighting Kakuzu, but a surprise back-up unit arrives on the scene to provide some much needed assistance.

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

In the aftermath of the battle, Teams 7 and 10 return to Konoha. After examining Naruto, Tsunade officially classifies Naruto's new technique as a Forbidden Jutsu and warns Kakashi never to let him use it again. What is the terrible secret of the Rasen Shuriken that has left even Tsunade stunned by its power? Meanwhile, Orochimaru orders Kabuto to search for a woman who will help him reach his goal.

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.

Kakashi leads Kiba, Hinata, and Shino on a mission to infiltrate Orochimaru's lair. What horrors and traps await them?

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.

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.

Kabuto assigns Guren to look after Yukimaru. Guren isn't all too happy about the assignment, and things only become worse when Yukimaru falls ill on a rainy night. Elsewhere, Kiba discovers the mystery of where the dog whistle is coming from, and Tsunade sends assistance to Kakashi and Team 8.

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.

While Naruto continues practicing a combo attack with Gamatatsu, Kakashi, Kiba, Hinata, and Shino have a run-in with Guren's gang. Will Kakashi and Team 8 be able to defeat these strange foes?

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 successfully breaks down the crystal labyrinth with his new jutsu and he and the rest of Team Kakashi come to Kakashi, Kiba and Shino's aide, and rescue Hinata as well. Meanwhile, Kabuto, Guren, Yukimaru and Gozu head to the lake Kabuto and Yukimaru went to before. What could be in the lake that Orochimaru wants?

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.

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.