Plot of Naruto: Shippūden

The plot of the second part of the manga and anime series Naruto, titled Naruto: in the anime and simply Part II in the manga, is set two and a half years after the present timeline in Part I. The new setting for the series begins with volume 28 (chapter 245) of the manga. The anime adaptation of the manga started airing on February 15 2007, premiering with the first two episodes debuting in a one hour special. The US publication of the manga will begin in January 2008, in the US issue of Shonen Jump.

The new story revolves mainly around Naruto's and Sakura's new adventures and their search for Sasuke Uchiha after he left Konoha to gain Orochimaru's power. The plot later involves new major characters, such as Sai and Yamato. The plot also shows a more active Akatsuki in their quest to obtain all the tailed beasts.

Reintroduction

 * This section covers chapters 245 to 247 in the manga and episodes 1 to 2 in the anime

To prepare for the eventual confrontation with both Akatsuki and Orochimaru, Naruto left the village and underwent intensive training under Jiraiya. At the same time, Sakura became Tsunade's apprentice, and Sasuke trained under Orochimaru. Thus, each of the three members of the original Team 7 were now training under one of the Legendary Sannin.

When Naruto returned to the village two and a half years later, he was reacquainted with his friends, who had all risen in rank in his absence. Most of his comrades had since become Chunin; Kankuro, Temari, and Neji Hyuga had become Jonin; Gaara had even become the Fifth Kazekage: Meanwhile, Naruto is the only Genin left aside from Sasuke, who never became a Chunin because of his leaving the village and becoming a Missing-nin. Jiraiya left Naruto with Kakashi Hatake, and along with Sakura, the three of them became a new team. To commemorate the event, they conducted another bell test, with Naruto and Sakura succeeding by telling Kakashi they would spoil the end of Itcha Itcha Tactics, forcing Kakashi to close his eyes and block his ears. When he opened his eyes he realized that Naruto and Sakura were holding the bells.

Rescue Gaara

 * This arc covers chapters 248 to 281 in the manga and episodes 3 to 32 in the anime

In Sunagakure, the Akatsuki team of Deidara and Sasori made their way to the village in search of Gaara. Deidara went off to fight Gaara alone while Sasori guarded the entrance. Gaara intercepts Deidara during the battle and managed to crush one of Deidara's arms using his Sand Binding Coffin. Despite his improved ability, Gaara's newfound desire to defend Sunagakure proves to be his downfall. When Deidara tries to destroy the village with his exploding clay, Gaara absorbed the blast by levitating the sand below. A direct attack by Deidara forced him to recall the sand which crushed Deidara's arm, which contains a small portion of exploding clay within. The clay then detonated, incapacitating Gaara.

After Deidara departed with Gaara, Kankuro attempted to stop the Akatsuki members alone, but his puppets were easily fought off and destroyed by Sasori, who is revealed to be the maker of Kankuro's puppets. Sasori poisons Kankuro in the process, leaving him to die. The Akatsuki duo take Gaara back to their lair, where their leader summons a giant statue to extract and seal Gaara's demon. The sealing ritual takes three days.

Upon hearing of Gaara's kidnapping, Team Kakashi left for Sunagakure with Temari, who was in Konoha to help with the most recent Chunin Exam as well as being the official Sunagakure representative to Konoha. On the way, Naruto tells Sakura and Temari that he is the host of the Nine-Tailed Demon Fox and that Akatsuki is after the demon inside Gaara. This gives Sakura some insight into what Naruto has gone through. After learning this she vows to do everything she can to protect Naruto from being a victim of Akatsuki. Temari is thankful that there is someone who can understand what Gaara has gone through, and she's grateful to Naruto for changing Gaara and attempting to save him.

At Sunagakure
After arriving at Sunagakure, Team Kakashi learned of the attack on Kankuro. Despite the failed attempt by the medics on-hand, Sakura cures Kankuro, thus demonstrating her skill with medical jutsu. Sakura also developed several portable antidotes rather quickly. Using a piece of Sasori's clothing found on one of Kankuro's destroyed puppets, Team Kakashi is able to track him, thus leading them to Gaara. Temari offered to assist them, but Chiyo, another puppeteer and Sasori's grandmother, went in her place. Back in Konoha, Tsunade decided to send Team Guy as backup for Team Kakashi. Gaara is then found dead.

While Team Kakashi tracked Sasori through a piece of torn clothing, the Akatsuki leader sent Itachi Uchiha and Kisame Hoshigaki to deal with Team Kakashi and the approaching Team Guy, respectively.

In a forest, Kakashi and Naruto were able to defeat Itachi after some effort using one of Kakashi's clones and Naruto's new Great Ball Rasengan, the clone being used to hold Itachi in place long enough for the jutsu to connect. Meanwhile, Team Guy was largely disabled by Kisame, leaving Guy himself to fight Kisame alone. Guy emerged victorious by opening six of the eight chakra gates to perform his Morning Peacock technique, which allowed him to pummel Kisame to death. However, both Akatsuki members were actually entirely different people in disguise. They were made into weaker copies of those they were impersonating through the leader's Shapeshifting Technique.

Despite their victories, the two teams realized their battles were distractions to buy time for Akatsuki to extract the Shukaku from Gaara, which will kill him if completed. At the Akatsuki hideout, a barrier was blocking the entrance. Directed by Kakashi, Team Guy removed the four seals maintaining the barrier, but a failsafe created clones of them as a further distraction. Ultimately, the many delaying tactics employed by Akatsuki are successful, as Naruto and Kakashi found Deidara and Sasori guarding Gaara's lifeless body. While Chiyo and Sakura fought Sasori, Deidara flew off on a clay bird with Gaara's body, with Naruto and Kakashi in pursuit.

Fighting Sasori
Although Sasori "wore" his puppets and controlled them from inside, this technique of puppeteer fighting soon proved to be futile against Sakura and Chiyo. By controlling Sakura like a puppet, Chiyo was able to get Sakura close enough to demolish the puppet with one punch.

With his first puppet destroyed, Sasori is revealed, looking just as young as he did when he left the village. He summoned another puppet to continue the battle: the Third Kazekage. It is here that Sasori reveals that he not only killed the Third Kazekage, but actually made his body into a puppet. Likewise, he has done the same to 297 other people. He planned to do the same to Chiyo and Sakura after winning. With its unique Iron Sand ability mixed with Sasori's poison, the Kazekage puppet is exceptionally dangerous. Chiyo summonned two more puppets to fight against it. These puppets were puppet versions of Sasori's parents, which he had made to remind him of them, because they left him early in his childhood. The puppets were left with the village when Sasori deserted it. At first, Sasori's Kazekage puppet proved to be more than a match for both Sakura and Chiyo, using its poisoned Iron Sand to disable both of them. However, the antidotes Sakura had developed earlier allowed them to continue fighting. Having been trained by Tsunade to pick up the enemy's attack patterns, Sakura was able to easily dodge Sasori's subsequent attacks and demolish the Kazekage puppet.

Down another puppet, Sasori reveals the secret of his youth: he made himself into a puppet. In this form, he had numerous weapons to fight with, and could even reassemble himself when destroyed, making him almost impossible to defeat. The only part of him that remained alive, and thus able to use chakra, was his heart, contained in a talisman labeled. In response, Chiyo used White Secret Technique: Ten Puppet Collection of Chikamatsu to summon Monzaemon Chikamatsu's ten masterpiece puppets. To mock the display, Sasori used his Red Secret Technique: Performance of a Hundred Puppets to summon 100 of his human puppets.

After a spectacular battle between the two puppet groups, one of Chikamatsu's puppets threw a chakra-sealing orb to Sakura to use on Sasori. Though it appeared successful at first, Sasori managed to abandon his body beforehand and take over a spare among the many puppets he had summoned earlier. Using the momentary distraction, Sasori stabbed Sakura with a poisoned sword. In doing so, however, he fell into a secondary trap created by four of Chikamatsu's puppets, which formed a seal on the ground. Sasori was now immobilized since he needed to use chakra to animate his puppet body, allowing Chiyo to use the mother and father puppets to stab him through his heart. In spite of the victory, Chiyo believed that Sasori allowed himself to be killed — he saw the attack coming and chose not to react, and died in a way similar to how his parents used to embrace him.

At the end of the battle, Chiyo, Sasori, and Sakura were all fatally wounded, but Chiyo used a jutsu she originally developed for Sasori to save Sakura's life. The jutsu uses the user's own life energy, making it fatal to use to animate a puppet, but Chiyo survives since Sakura was still alive. Sasori's last words (as a reward to Sakura for defeating him) are that he has a spy in Orochimaru's ranks, whom he is supposed to meet in Kusagakure in ten days.

Fighting Deidara
Meanwhile, Naruto and Kakashi chase after Deidara. Kakashi activated his own version of the Mangekyo Sharingan, but it is difficult to aim properly and only managed to remove Deidara's remaining arm (Kakashi was aiming at his head). Naruto managed to destroy the clay bird using his Rasengan and retrieved Gaara's body. Enraged, Naruto sent a demon-fox-powered clone to attack Deidara, who attempted to get away since he no longer had any arms. The clone was able to defeat Deidara by creating more clones, but this Deidara was also a clone. Still enraged, Naruto started to appear feral as two tails of chakra begin to form, causing his clones to experience a burning sensation in their stomachs. Kakashi recognizes this as a bad sign and used a special seal he received from Jiraiya to stop the transformation from proceeding any further. Naruto subsequently reverted back to his normal form.

As the rest of Team Kakashi and Guy caught up with Naruto and Kakashi, Neji spotted Deidara attempting to escape. Cornered, Deidara moved to the remains of his bird and swallowed some of the clay, turning himself into a human bomb. Neji realized what was about to happen and quickly directed the group to leave, fearing that not everyone would get away in time. As the dust settled, Kakashi collapsed from exhaustion, explaining that he used his Mangekyo Sharingan to send Deidara to another dimension. With Naruto carrying Gaara's body, the two teams headed back to Sunagakure.

Epilogue
Stopping in a grassy field near the village, Sakura checked on Gaara and pronounced him dead. Naruto grew very upset, lashing out verbally at Chiyo. As he began to cry, Chiyo moved towards Gaara and tried to use her resurrection technique, but didn't have enough life force left. Naruto gladly lent his own chakra, and Chiyo was able to revive Gaara at the cost of her own life while the shinobi of Suna looked on.

Back at the battleground, Deidara emerged from the ground, revealing that it was his clone that destroyed itself. He went off looking for the right arm that he lost. After finding it, he encountered Zetsu and Tobi, a mysterious individual who wished to take Sasori's place in Akatsuki. Tobi's carefree attitude about Deidara's condition angered Deidara, and he attempted to strangle Tobi with his feet after one-too-many callous remarks.

After paying their respects to Chiyo, and bidding Gaara and his siblings farewell, the Konoha shinobi returned home. Kakashi was still exhausted from his overuse of his Mangekyo Sharingan and had to be carried back by Guy. Guy does so piggyback style, disturbing everyone present except Lee, who remarked that Guy was training. Lee then proceeded to offer to carry Neji, who bluntly refused.

Gaara is still able to control sand but it is unknown whether the loss of Shukaku has affected his usual attacks. Supposedly, the sand no longer acts on its own accord to create its usual barrier around him.

Exposition

 * This section covers chapters 282 to 284 in the manga and episodes 33 to 34 in the anime.

When they arrive at Konoha, Kakashi is confined to the hospital and is unable to lead the team until he recovers. Naruto searches the village to find a possible replacement, as well as a third team member. During this time, he meets Shino, Kiba, Hinata, Choji, and Ino again.

Naruto meets his "third man" before actually learning who he is. While talking with Choji and Shikamaru, the ninja, later introduced as Sai, attacks them and is warded off by the trio. Sai was sent by Danzo to replace Sasuke. Sai is a member of the now-defunct independent subdivision of ANBU called Root.

It is also discovered that some of the village elders are worried about the possibility of Naruto being captured by Akatsuki. Tsunade convinces them to let him go by assigning Yamato, an ANBU captain, as the temporary leader of Team Kakashi. They are to travel to the World Bridge in Kusagakure to meet Sasori's spy.

Sai and Sasuke

 * This arc covers chapters 285 to 310 in the manga and episodes 35 to 53 in the anime.

Encounter with Orochimaru
from episode 40 to 46. Team 7 takes on their new mission, and a great amount of tension begins to build in the team, especially between Naruto and Sai. Naruto dislikes Sai since their interactions are similar to those between himself and Sasuke in the beginning of the series. Making matters worse, Sai nonchalantly mentions Sasuke's treachery, greatly irritating both of his teammates to the point that Sakura punches him in the face.

Yamato, disguised as Sasori, goes to meet the spy. The spy is revealed to be Kabuto Yakushi, but the jutsu binding him to Sasori had been dispelled long ago. Orochimaru appears and attacks Yamato, destroying the disguise. Orochimaru reveals that he had performed experiments on Yamato and 59 other children, giving them the First Hokage's DNA in an attempt to replicate his Mokuton kekkei genkai. Yamato was the only survivor. Orochimaru then calls out the rest of Yamato's team and taunts Naruto by speculating whom is now stronger: Naruto or Sasuke. Naruto, provoked by the mere mention of Sasuke's name, transforms first into his three-tailed fox state, then into four-tailed state shortly thereafter.

It is revealed that during the time skip, Jiraiya was nearly killed by Naruto's four-tailed transformation. The demon fox's chakra becomes so intense that it simultaneously burns Naruto's skin and rapidly heals the burnt tissue. This speeds up cell division dramatically, decreasing Naruto's overall life span.

In his four-tailed state, Naruto fights Orochimaru to a draw. In the end, Orochimaru was only able to throw Naruto back to the bridge Naruto is unable to distinguish friend from foe and attacks Sakura when she tries to calm him down. Yamato finally gets close enough to use Hokage-Style Sixty-year-old Technique: Enclosed Hermitage Return to Society, a demon-controlling technique, to revert Naruto back to human form.

With Naruto's transformation reversed, Sakura uses her medical skills to heal Naruto's severe injuries, still suffering herself from her previous injury. Though Sakura is upset at how little she can do, Yamato states that it is the strength of her feelings for Naruto that matters most.

Meanwhile, Sai reveals to Orochimaru that he is a messenger from Danzo. Sai, Orochimaru and Kabuto leave to a secret hideout. Yamato watches the encounter with a wood clone and pursues Sai. Yamato is not fooled when he finds a decoy disguised as Sai's corpse.

Naruto wakes up to find Sakura injured and the surrounding landscape destroyed. Yamato steps in to inform Naruto about the real cause of the destruction when Sakura hesistates to tell Naruto the real cause of her injury. In addition, Yamato tells Naruto that the only way to save Sasuke and protect the village is to rely on his own chakra, not that of the demon fox.

Meanwhile, Sakura goes through Sai's belongings and finds his art book. The sketchbook contains drawings of Sai and what the team assumes is his older brother growing up and going through a gauntlet of enemies. On each subsequent page, Sai takes the weapons and armor of his previous opponent. The center pages, where the two brothers are supposed to meet, are unfinished.

At Orochimaru's hideout, Yamato reveals that he was able to track Sai through a special plant seed hidden in his breakfast. He gives Sakura and Naruto similar seeds to make sure they can find each other if separated. Once inside, Yamato leads the team to a room where Sai is being kept hostage. Sai tries to lie about his mission, but an accidental smile allows Naruto to call his bluff. Sai then states that his mission is a failure and confirms that Danzo is indeed planning another strike at Konoha. However, he is also acting as a spy for Danzo, since Danzo knows as soon as Konoha is destroyed, Orochimaru will turn on him. Sai disapproves of rescuing Sasuke, saying that Sasuke doesn't see Naruto as a brother and that Orochimaru is too powerful for them. Naruto replies that he and Sasuke have a special bond, and that he will fight Orochimaru with everything he has to get Sasuke back, even if it means sacrificing his own life.

At this point, Kabuto shows up and frees Sai, but Sai shocks everyone by helping Yamato immobilize Kabuto. Kabuto is forthcoming, providing information on the interior of the lair, but not Sasuke's actual location. Team Kakashi splits up to search for Sasuke, with Naruto teaming with Sai and Sakura with Yamato. Naruto, still tired from his injuries, collapses, and Sai suggests taking a rest; Naruto is notably less hostile towards Sai at this point. Sai begins to talk about his brother, who resembles Naruto. The short chat soon ends as Orochimaru appears. Naruto tells Sai to find Sasuke while he holds off Orochimaru. As Yamato and Sakura arrive to back Naruto up, Orochimaru again mentions that he does not wish to kill them since both parties oppose Akatsuki. Orochimaru then leaves in order to locate Sai. Yamato finds a "Bingo Book" (a list of people who are marked for assassination) in Sai's bag, with Sasuke's name in it. Naruto and Sakura realize that another part of Sai's mission is to kill Sasuke, who had been listed as an enemy of Konoha by Danzo. Naruto is speechless, realizing that Sai has duped him with his "fake smiling" act.

Sai manages to find Sasuke in his room, and wakes him up. Sasuke, angry at Sai's mention of "bonds", blows up the room. Sakura spots Sai in the hallway and runs to him. Though she means to attack Sai, Sasuke quietly says Sakura's name, stopping her in her tracks. Naruto, in his weakened state, finally catches up, coming face to face with Sasuke again.

Meeting Sasuke Again
from episode 47 to 53. As Sasuke observes the new Team Kakashi, Sai explains to Naruto and Sakura that his desire to protect the bond between Naruto and Sasuke has overridden the mission Danzo gave him. Sasuke replies that he has broken his bond of friendship with Naruto and that the only bond he has left is a bond of hatred.

As both Sai and Yamato move to try and protect Naruto, Sasuke uses Chidori Current, which projects electricity around his body and his new Kusanagi, to repel them. He manages to stun Naruto and Sai, then wound Yamato. As Sasuke fights Yamato, Naruto undergoes a partial demon fox transformation. In Naruto's mind, the imprisoned demon fox implores him to release the seal. When Naruto refuses, the demon scoffs, saying Naruto has always come to him in times of need and that Naruto is worthless without his power. Suddenly, Sasuke appears in front of the demon fox, stunning both of them. Sasuke marvels at the source of Naruto's power. As Sasuke begins to push the demon fox back into its cage, the demon fox then remembers his past history with the Uchiha clan. He states that Sasuke may possess chakra even more evil than his own, "just like that Madara Uchiha." The fox also warns Sasuke not to kill Naruto, stating that he would regret it.

Outside of Naruto's mind, Yamato pushes the sword out of his wound and tries to trap Sasuke in a wooden prison. Sasuke blows a hole through the roof of the prison to escape. Naruto yells out to Sasuke that Orochimaru just wants to use Sasuke as the next container for his soul, but Sasuke doesn't care as long as it helps kill Itachi. Yamato then tells Naruto and Sakura that he didn't want to hurt Sasuke in front of them, but he has no choice and will finish the confrontation. Sasuke plans to do the same, but Orochimaru returns just in time to stop Sasuke from performing a jutsu. Kabuto tells Sasuke to leave the Konoha shinobi alive so that they might oppose Akatsuki. Sasuke tells Kabuto that's a poor excuse to not kill Naruto, but leaves with them anyway. Naruto is upset by the meeting and by how weak he is in comparison to Sasuke, but Sakura and Sai both assure him that they will help bring Sasuke back.

The team reports back to Konoha, during which Naruto tells Tsunade that they have not given up and will continue. Pleased by this response, Tsunade assigns the team a new mission. Sai reports to Danzo, who is displeased that Sai has failed his mission. Sai asks to remain with Team Kakashi and Danzo warns Sai that developing emotions will only lead to hatred and conflicts. Sai has flashbacks of recent events, ponders his own feelings, and realizes that he now has friends. Sai adds a title ("Friends") to a picture in front of his window, the first picture he has ever given a title. Having reclaimed his emotions, he heads off with Naruto, Sakura, and Yamato to begin their new mission.

Hidan and Kakuzu

 * This arc covers chapters 311 to 342 in the manga.and episodes 72 to current in the anime

Akatsuki activity
Two newly introduced Akatsuki members, Hidan and Kakuzu, are chasing after the host of the two-tailed cat, Yugito. Despite fully transforming into her two-tailed state, Hidan and Kakuzu defeat Yugito. After the battle, Hidan performs a gruesome religious ritual, greatly annoying Kakuzu, a money-obsessed bounty hunter. Zetsu appears and takes charge of Yugito, ordering the pair to proceed to the Land of Fire and their next target.

Hidan and Kakuzu stop by a nearby temple and kill the head monk Chiriku, a former bodyguard for the Land of Fire's nobility. One monk manages to escape and informs Tsunade of the incident. Tsunade orders Shizune to mobilize a new task force, the Niju Shotai. Asuma's group, consisting of himself, Shikamaru, Kotetsu Hagane, and Izumo Kamizuki, leaves for the temple.

Team Asuma arrives at the ruins of the temple and realizes that the Akatsuki pair has taken Chiriku's body to a bounty station. The team prepares to intercept the killers at the station, and a monk prays for the team's safety. When the monk expresses concern for their safety, Asuma reveals that his bounty is five million ryō higher than Chiriku's. Meanwhile, Hidan and Kakuzu collect the bounty on Chiriku's head and turn over the corpse as proof.

Elsewhere, Deidara, having regained his limbs and now paired with Tobi, confronts the three-tailed beast. Tobi acts strangely flippant before the battle with the immense aquatic beast. After subduing the monster, Tobi claims he single-handedly won the battle, provoking another comedic attack from Deidara.

Training Naruto
After the encounter with Sasuke, Naruto realizes that Sasuke is far too strong for him. Kakashi reveals a special training method which takes advantage of Naruto's high chakra. It involves the Multiple Shadow Clone Technique. Unlike an ordinary clone, a shadow clone passes back any experience it gains to the original. Naruto can create a comparatively large number of shadow clones, thus allowing him to train hundreds of times faster than a normal shinobi. Yamato also assists in Naruto's training by helping to restrain the demon fox.

Kakashi explains that there are five basic types of elemental chakra — fire, wind, water, lightning and earth. He pulls out special cards which react differently to each person's chakra: it will burn for fire, split for wind, crumple for lightning, turn to dust for earth, and turn wet for water. Naruto flows his chakra into the card and it splits, indicating he has an affinity to wind, a type that is very well suited for combat because of its ability to "blow past anything and slice things to bits."

Meanwhile, Asuma and Shikamaru are playing Shogi. Shikamaru notices that Asuma is playing differently from normal and asks if something is wrong. In describing things, Asuma describes Shikamaru in terms of shogi as a Knight, being weak in terms of power but having a unique style of movement that resembles Shikamaru and his flexibility in his thinking. Shikamaru then asks what piece Asuma resembles. Asuma then answers that he is just a pawn. Shikamaru guesses that the Hokage is the king, but Asuma tells him that it's not, and that someday Shikamaru will understand.

The first phase is for Naruto and his clones to cut a leaf with his chakra. Naruto asks if there's anyone in Konoha that can help him, and Kakashi tells him to find Asuma. Asuma gives Naruto a few pointers using his trench knives as an example. They're made of a metal that absorbs chakra, the effect of which is determined by the user's chakra nature. Asuma explains that wind chakra must be sharpened like a blade by splitting the chakra in two and bringing the parts together to form a tight edge. He demonstrates this by having Naruto toss a knife at a tree with him: Naruto's sticks in the tree while Asuma's goes straight through it and pierces a rock.If he had used his full chakra, the knife would have also gone through the rock. Using this advice, Naruto is able to completely split a leaf, but passes out after dispersing his clones. Kakashi warns him that this training is going to wear him down quickly, and that he needs to rest for the next phase of his training: slicing a waterfall in half.

The next step of Naruto's training progresses slowly. When Naruto complains, Kakashi notes that even Sasuke took several days to learn to manipulate an element, while Naruto did it in a few hours. By nightfall, Naruto hasn't managed to cut the waterfall. Naruto reflects on his fonder memories of Sasuke and decides to train through the rest of the night. By the next day, he and all his clones are able to cut the waterfall. Yamato is surprised by Naruto's progress, but Kakashi is not, since he understands how Naruto feels about Sasuke. Kakashi declares they can finally move into the final stage of Naruto's unique jutsu creation. However, the constant training has exhausted Naruto once more. Kakashi immediately rushes to his side concerned that he may have pushed Naruto too far this time. However, when Naruto moans that he's hungry, Kakashi relaxes.

After enjoying a meal at Ichiraku Ramen, Naruto is anxious to go on with his training. Kakashi and Yamato explain "nature manipulation" and "form manipulation" to Naruto again. Kakashi reminds Naruto that all the training till now has been nature manipulation and that the Rasengan is an example of extremely advanced form manipulation. By adding nature manipulation together with form manipulation, a ninja's power can grow by leaps and bounds. However, this is an extremely difficult task; even the Fourth Hokage was unable to complete the Rasengan by combining nature and form manipulation. Kakashi believes that Naruto is the one who will finally surpass the Fourth Hokage. As the two Jonin leave, Yamato commends Kakashi for his smooth talk. Kakashi corrects him, saying that he sincerely believes in Naruto.

Akatsuki vs. Niju Shotai
At the bounty station, Kakuzu explains that Hidan, an immortal, is the only ninja capable of surviving Kakuzu's indiscriminate attack strategies. This is the reason for their partnership, despite their ideological differences.

As Asuma's group moves toward the bounty station, Asuma explains that he and Chiriku both belonged to the 12 Guardian Ninja of Konoha, and that their relationship was akin to Shikamaru's relationship with Choji. Asuma stopped smoking because he needs no distractions if he is to fight Chiriku's killers.

Naruto is again training with his clones, trying to infuse the Rasengan with wind chakra. Unfortunately, the jutsu consistently explodes, frustrating them to such degrees that a clone will start drawing upon demon fox's chakra. Yamato reverses the transformations, and Kakashi reminds him that success or failure rests on Yamato's ability to control the demon fox.

At the bounty station, Asuma's team attacks Hidan. Izumo and Kotetsu stab him in the chest with their large kunai; however, Hidan is merely annoyed by the attack. Asuma's team quickly realizes that Hidan cannot be killed by normal means. Kakuzu appears and prepares to join the fight, but Hidan tells him to stay out of it. Asuma proceeds to fight Hidan alone. Hidan manages to cut Asuma's cheek and licks the blood off his scythe just as the latter uses a fire jutsu. Hidan draws a seal beneath him just as the jutsu hits. It burns Hidan's robe, but he emerges unscathed. Instead, Asuma's right arm is badly burned; the damage meant for Hidan has somehow been turned back upon himself. Hidan has also transformed; his skin is black with white accents, giving him the appearance of a Grim Reaper. Hidan tells Asuma that any pain he feels is transferred to Asuma. Since he's immortal, Hidan needs only to inflict a fatal wound on himself to kill Asuma.

Luckily, Shikamaru catches Hidan in another Shadow Bind before he can do so. Kakuzu offers to help, but Hidan waves him off, claiming he can beat all four by himself. Going over every motion Hidan made to start the ritual, Shikamaru figures out Hidan's ability: Hidan first needs to consume his opponent's blood and then stand within his ceremonial circle. Shikamaru explains that in order to save Asuma, all he needs to do is move Hidan out of his circle.

After Shikamaru tests his theory, he traps Hidan with Shadow Sewing. Hidan asks Kakuzu to help him, but Kakuzu nonchalantly replies that he told Hidan to be careful. Asuma slices Hidan's head off with his chakra blades, and it falls next to Kakuzu. Rather than killing Hidan as expected, the head starts talking, calling Kakuzu a bastard for allowing him to be decapitated. Hidan asks Kakuzu to bring him his body, but Kakuzu grabs his head instead, saying that it is lighter.

Shikamaru falls from exhaustion as Hidan complains about the pain of being decapitated. Asuma, Kotetsu, and Izumo stand in amazement and plot their next move. Kakuzu suddenly attacks Asuma, then grabs Hidan's body. He reattaches Hidan's head using threads from his arms. Kotetsu and Izumo attempt to strike Kakuzu, whose forearms extend, grabbing both of them by the throat. Meanwhile, Hidan jumps back into the circle, linking himself back to Asuma, and deals himself a fatal blow to kill Asuma.

Asuma collapses as his team looks on helplessly. Hidan reverts to his normal form as Kakuzu prepares to finish off the others. A flock of crows suddenly appear, distracting the Akatsuki pair. Ino and Choji appear to assist in moving Shikamaru and Asuma to a safer location as Aoba Yamashiro and Raido Namiashi back them up. Shikamaru senses Asuma's pulse, and tells Ino and Choji to take him back to Konoha. Kakuzu isn't willing to let a bounty like Asuma go, and Hidan is similarly unwilling to let his enemies live, but the Akatsuki leader contacts them telepathically and forces the pair to retreat, wanting to seal the three-tailed beast Tobi and Deidara recently captured.

Despite the timely rescue, Asuma's wounds are fatal. Asuma dies, but not before smoking his last cigarette and sharing some final words with Ino, Shikamaru, and Choji. Shikamaru lights another of his cigarettes, which he begins to smoke himself. He tearfully mumbles that he hates cigarettes as they make his eyes water — a reference to when Team 10 first met their sensei.

As Akatsuki commences with sealing the three-tailed beast, the leader explains their goals to Hidan and Tobi. Akatsuki's overall goal is world domination. To achieve that goal, the leader has set up a three-step process to work their way to it. First, they plan to obtain a large amount of money to support their organization. Second, they plan to set up a mercenary group loyal to no village. Because there haven't been any wars in some time, they can convince the smaller countries to hire them over the larger asking prices of the five main villages. By using the tailed beasts, they can start wars and then immediately quell them, convincing every country to depend on them and monopolizing the shinobi market. Finally, after they're the only major force of shinobi in existence, they can easily conquer the world.

Team 10 returns to Konoha and informs Tsunade of what had happened. Tsunade sends out the message for the funeral to everyone, but Shikamaru has a message for Kurenai from Asuma and will tell her what has happened himself. Naruto has nearly created the jutsu when they are informed of Asuma's death and rush back to the village. Shikamaru tells Kurenai the message and she collapses from grief. At the funeral, Konohamaru cries for his uncle while Naruto comforts him. Shikamaru doesn't attend the funeral and spends his time seemingly formulating a strategy and learning how to use Asuma's trench knives. He also picks up Asuma's smoking habit.

Akatsuki vs. Team 10
The new three-man Team 10 prepares to leave and continue Asuma's mission. Tsunade refuses to let Team 10 go since they lack a captain. Kakashi volunteers, and the four-man team heads off. Later in the woods, Shikamaru devises a new attack strategy that includes Kakashi.

About three days later, Sakura volunteers her team to back up Team 10. Tsunade tells Yamato that Naruto has 24 more hours to complete his new jutsu, or she will send another Team as backup.

After Akatsuki finishes sealing the Sanbi and Nibi, so Kakuzu and Hidan are allowed to leave. Realizing the likely ambush, Hidan and Kakuzu take another route. Ino uses her Mind Body Switch Technique on a crow and finds the two. Team 10 then goes to ambush the Akatsuki.

Shikamaru sneaks his shadow near Hidan and Kakuzu, who both manage to jump out of the way. However, Shikamaru manages to pin their shadows in place using Asuma's chakra knives to extend his shadow. However, Kakuzu thought a step ahead, and detached his arm, so he sends it to attack Shikamaru, forcing Shikamaru to release the shadow. Kakashi leaps out and hits Kakuzu with a Lightning Blade. However, Kakuzu uses his Earth Element defense to harden his body as a shield but Kakashi's lightning blade manages to peirce through Kakuzu's heart. Thinking he won Kakashi lowered his guard and Kakuzu got up and kicked Kakashi away. It was then Kakuzu took off his Akatsuki cloak and revealed four animal masks on his back with one destroyed.

It turns out that Kakuzu has a total of five hearts, four of which were stolen from the body of a fallen shinobi, and the one that allows him to use his Earth Element attack is his. Each heart prolongs Kakuzu's life and allows him access to the heart's elemental affinity. Hidan attacked Kakashi as a distraction which allowed Kakuzu enough time attack with a powerful gust of wind. He then fired two powerful bolts of lightning at Shikamaru and Choji but Kakashi blocks it with a Lightning Blade in each hand. He then attacked with fire which was dodged by Team 10 and Kakashi. Shikamaru decides to separate Hidan and Kakuzu from each other.

Once again capturing Hidan with a Shadow Imitation jutsu, Shikamaru drags Hidan to an isolated location rigged with booby traps. However, Shikamaru's chakra runs out, which frees Hidan from the jutsu. Hidan successfully attacks him and begins the voodoo ritual.

Kakuzu reveals that the first Konoha ninja he ever fought was the First Hokage. As Kakashi is about to be killed, Kakuzu grabs his chest in pain. This is due to Hidan stabbing himself as part of his curse ritual: the blood he consumed was actually Kakuzu's.

Team 7's Arrival
Hidan does not immediately realize what has happened, but Shikamaru attacks him to illustrate the point. However, Shikamaru is weakened from the extended use of his shadow jutsu and cannot hold down Hidan for long, he watches Hidan advance to strike the final blow.

Kakuzu continues battling Kakashi. However, as Kakuzu prepares to strike with his Wind Element attack, Naruto intervines and uses his Wind Element: Rasengan to block the attack.

Kakashi, Ino, and Choji are relieved at Team 7's arrival. Yamato orders Sai and Sakura to back Shikamaru up, and Kakashi summons Pakkun to lead them. Naruto resolves to defeat Kakuzu on his own.

Hidan fails to kill Shikamaru, as the latter ensnares him with a shadow once more. Having prepared the area in advance, Shikamaru uses his shadows to pull the explosive tags onto Hidan, and open a deep pit beneath him. Hidan insists that he'll survive the attempt, even if only his head remains intact, and kill Shikamaru in turn. Shikamaru calmly explains that they are on his clan's land, and that his clan will keep Hidan buried for eternity. Lighting a cigarette, Shikamaru sees a vision of Asuma, who congratulates him before disappearing. Saying his last goodbye, Shikamaru tosses the lit cigarette at Hidan, igniting the explosive tags and causing a massive explosion. Hidan survives the explosion, and insists that he will "bite" Shikamaru to death, all the while proclaiming that his god Jashin will punish Shikamaru. Shikamaru ignores the threats and tosses a kunai with exploding tags into the hole. The explosion causes the hole to cave in, burying Hidan in rubble.

Meanwhile, Naruto uses his Wind Element: Rasengan to block one of Kakuzu's Fire Element attacks. Naruto then begins preparing an extremely powerful jutsu. Kakashi realizes through a flashback that Naruto may indeed surpass the Fourth Hokage. Naruto then uses his Wind Release: Rasenshuriken. Kakuzu is visibly concerned by the new jutsu.

Kakuzu jumps into the air, but Naruto leaps behind him. Kakuzu is forced to sacrafice four of his hearts, and through that he is able to shield against the attack using his Earth Element shield. However, this leaves him unable to move. Kakashi realizes Naruto has surpassed him, and goes to finish Kakuzu by stabbing his last heart.

Team 7 and Team 10 return triumphant to Konoha. Shikamaru visits Asuma's grave with Kurenai, who is now pregnant with Asuma's child. Later, while playing shogi with his father, Shikamaru comments that the identity of the king piece is the next generation of Konoha ninja. Despite this revelation, he loses the game with his father.

Hunt For Uchiha arc

 * This arc covers chapters 343 to 402.

Sasuke vs. Orochimaru
At Orochimaru's lair, a sick Orochimaru is confined to his bed. As Kabuto exits to get more medicine, a blade made of lightning chakra shoots towards Orochimaru through the door. Orochimaru quickly blocks it with his arms and thinks to himself that he does not recognize the shape manipulation, though the chakra itself seems familiar. The blade belongs to Sasuke, who had stopped by to finish Orochimaru off before he left to take on Itachi. He claimed that he had nothing more to learn from Orochimaru and mocks him for wasting his power and time, which angers Orochimaru.

After pinning Orochimaru's arms to the wall, Sasuke attempts to deliver a finishing blow, forcing Orochimaru to ditch his body, revealing his true form: a composite serpent-like entity made up of small white snake. Sasuke activates his Cursed seal Level 2 and begins to fight Orochimaru on even. He compares Orochimaru's ambitions to how a snake dreams of flying and tells him that he will get that chance in the talons of a hawk, as he sprouts his curse seal wings.

After he severs Orochimaru's head from his body, Sasuke believes he has won. However, Orochimaru's poisons paralyze Sasuke, and he then lunges at him, swallowing him whole. Sasuke finds himself inside Orochimaru: the place where the body-transfer jutsu takes place. Orochimaru relives a flashback of when he confronted Itachi while in Akatsuki. He finds Sasuke's eyes to be similar to those of Itachi's on that day, and anticipates taking possession of those eyes. After the fight, Kabuto returns with the medicines, but views a scene consisting of Sasuke standing over Orochimaru. Kabuto asks Sasuke which one he is, to which Sasuke replies by showing Kabuto what happened. Sasuke states that he has merely taken over.

Recruiting "Snake"
After defeating his mentor, Sasuke frees Suigetsu, whom Orochimaru had imprisoned in a glass tank filled with water. Sasuke leads Suigetsu to the Land of Waves to retrieve Zabuza Momochi's sword from his grave. Upon their arrival, Sasuke notices the bridge that was being built during his time there, now named The Great Naruto Bridge. Suigetsu picks up the sword at Zabuza's grave and explains that he trained under the Seven Ninja Swordsmen (which his senpai, Zabuza, belonged to). With the sword, he claims, he might even be able to beat Sasuke. After collecting it, they head for their next target.

After arriving at the base, Sasuke and Suigetsu meet Karin, who sensed their arrival. Sasuke tells Karin to join him, which surprises her. Sasuke replies that since Orochimaru is now gone, there is no need for her to continue to keep watch over the prisoners she is currently guarding, telling an annoyed Suigetsu to free them. Karin relents, but still refuses to go. Sasuke decides that he will just have to find someone else. However, Karin has a quick change of personality and agrees to go if he really wants her to. Suigetsu advises they leave since Karin clearly doesn't want to go. When Sasuke says she's changed her mind, Karin puts her glasses back on and denies this in a rather embarrassed manner, saying that she's coincidentally going the same way they are, at least for the moment.

As the three make their way to the North Hideout, Karin explains that Sasuke's next target, Jugo, is the means behind Orochimaru's development of the cursed seals. When the group gets there, prisoners infected with the cursed seal surround Sasuke's group. When Karin informs them that Jugo is not among the prisoners, Sasuke and Suigetsu dispose of them without killing them (something Sasuke suggests). Having found the keys to Jugo's cell, Karin uses her tracking ability to find him, misleading Suigetsu to the wrong direction while she is at it. At Jugo's cell, Karin unlocks the door, and Sasuke goes in first. Jugo, who had decided that if the first person to open the door was a guy, he'd kill him, seems delighted to see Sasuke and rushes in for the kill. Sasuke fails in his attempts to reason with Jugo. Jugo and Sasuke have a quick cursed-seal battle, before it is interrupted by Suigetsu. Suigetsu then appears to take over the fight, explaining that beating Jugo to a pulp is the only way to calm him. Jugo morphs his piston arm into a massive forearm blade to deal with Suigetsu. After they ignore Sasuke's requests to stop, Sasuke wraps the two in summoned snakes and exudes an enormous amount of murderous intent. Jugo's transformation recedes, and he suddenly rushes back to his cell, demanding they lock it. Karin explains that while the rage-driven Jugo may be violent and bloodthirsty, Jugo himself has no desire to harm anyone.

Jugo finally agrees to go with Sasuke after hearing that Kimimaro, who was consistently able to stop Jugo's rage-driven rampages, died to bring Sasuke to Orochimaru. With his team gathered and dubbed "Snake" by Sasuke, Sasuke reveals their goal: to kill his brother Itachi. Suigetsu, who wants to take Kisame's sword for himself, is willing to participate. Karin, being enamored with Sasuke, also agrees to help, though she is unwilling to admit that her admiration is the reason. (Suigetsu teases her about it, saying that he knows about something Karin did to Sasuke long ago. However, Karin punches Suigetsu in the face before he can reveal her secret.) Finally, Jugo acquiesces to see how strong Sasuke is, believing he is Kimimaro's reincarnation.

Sakura arrives at Naruto's home to tell him to wash up and get ready. They meet up with Tsunade and Jiraiya, and Tsunade informs them of Orochimaru's death at Sasuke's hands, which Jiraiya's most trusted sources have confirmed. Both Naruto and Sakura seem very happy to hear the news, expecting that now that Orochimaru is dead, Sasuke will finally return to Konoha. However, Jiraiya tells them that is not exactly the case.

Hunt for Itachi Uchiha
In Konoha, Naruto and Sakura come to the same conclusion as Sasuke, reasoning that his desire for revenge will drive him to kill Itachi. Therefore, they decide the simplest path to Sasuke is to find Itachi. As both teams resolve to find Itachi, both he and Kisame wait for the leader to contact them after having captured the host of the four-tailed beast. Once they get into contact with their leader, Akatsuki goes over the recent deaths of Hidan, Kakuzu, and Orochimaru, and Sasuke's new team. Knowing that Sasuke could potentially disrupt their plans, the leader warns everyone to be careful, especially Itachi and Kisame.

In Konoha, Kakashi discusses the overall plan to find Itachi and Kisame. Since simply killing Itachi first would make finding Sasuke impossible, they need to capture him. For that purpose, Team Kakashi is joined by Team 8. Meanwhile, Sasuke takes his team to an old Uchiha outpost run by allies of the Uchiha Clan to stock up on supplies. After Akatsuki finishes sealing the four-tailed beast, Deidara and Tobi decide to either track down Kakashi and Naruto or go after Sasuke.

As Deidara and Tobi search for either of their two targets, the two teams split up. The Konoha ninja split into groups of three: one ninja and two of Kakashi's Ninken. Naruto is accompanied by Hinata and Yamato due to Akatsuki's pursuit of him. Meanwhile, Sasuke's group splits up to gather info on Akatsuki. As they search, the Ninken accompanying Sakura catch Sasuke's scent. Her search leads her into a city, but she is unable to find Sasuke. As she walks through a crowd, the ninken comments how the scent is "moving away," right as Karin is walking by her.

Kabuto reveals himself to Naruto's group, and gives them a book that details everything they learned about Akatsuki. He thanks Naruto for inspiring him to find his own purpose in life, and reveals that he absorbed Orochimaru's remains into himself: about 33% of his body is now Orochimaru's. With it, he plans to become stronger than Orochimaru. After evading Naruto and Yamato, he explains that he needs to control Orochimaru's power, which is slowly taking over his body, after which he will come after Sasuke for killing Orochimaru, and then Naruto.

Sasuke vs. Deidara
Elsewhere, Deidara and Tobi attacked Sasuke. Deidara attempted to attack from above using a bomb, but Sasuke used Hidden Snake Hands to wrap himself with a snake as a shield. Tobi also attempted an attack, but he was scared of Sasuke and ran from him. Deidara told Tobi he was to handle Sasuke, and tested him with small C-1 spiders. Sasuke used the Chidori Current in the form of small needles to stop the bombs. He then jumped behind Deidara, who used a bomb to distance himself. But Sasuke used Soft Physique Modification to absorb the bomb's power. Realizing Sasuke's abilities are great, Deidara used C-2 next, and summons a clay dragon as a battle partner. Sasuke uses his Chidori Current, Soft Physique Modification, and Hidden Snake Hands to stop the bombs, and has a few short hand to hand combats with Deidara. He forces Deidara to go a higher level in a short time though. He shoots two giant shurken at Deidara. Deidara avoids them, but Sasuke attached wires to them. They impale and hit the dragon, and Sasuke flies up with his sword and cuts the dragon's wing and cuts its head off. Deidara falls to the ground, and is impaled with the two shuriken in his arms. Tobi cries out for Deidara but Deidara tells him to be quiet. He looks into Sasuke's Sharingan eyes and remembers when he first saw them in Itachi. He was once approached by Itachi, Kisame, and Sasori for a proposal. Deidara was chosen to be on Akatsuki, but refused, loving his position as a terrorist bomber, claiming his works as art and as invincible, and how their beauty comes when they explode. Sasori is interested in Deidara for being an artist and having guts, but claims he is arrogant and can get himself killed quickly. Itachi decides to fight Deidara, claiming if Itachi wins, Deidara joins Akatsuki, but if he loses Deidara is free to go. Itachi shields himself from Deidara's bombs with Shadow Clones, and after a short fight, finishes him off with a Sharingan genjutsu, making it seem like Itachi has gained control of Deidara's bombs, and is about to finish Deidara with one. He stops the genjutsu and frees Deidara, but Deidara still is still forced to join for his loss. Deidara is angered at Itachi and the Sharingan, refusing to accept it as an art. In his fight with Sasuke, Deidara uses C-4, his most powerful bomb. It explodes and appears to have killed Sasuke, but it is simply a Sharingan genjutsu from Sasuke, the same one Itachi used. Sasuke then appeared to have constricted him with one of his bombs, but the genjutsu is dispelled by Deidara, as he reveals his left eye can dispel genjutsu, and since Sasuke held back when using the technique, unlike Itachi, Deidara was able to dispel it. Deidara tried another C-4 on Sasuke using his last bit of chakra, and went to a safe distance, but Sasuke shielded it one last time with his Chidori Current. He then jumped right next to Deidara and gave him a powerful punch to the face. Realizing that Deidara was out of chakra and could not move, Sasuke asked where Itachi was. Deidara did not answer, and became insane due to Sasuke's abilities being too much for him, and because of Sasuke's indifference towards Deidara's art. He then turns himself into a bomb in a suicide attempt to kill Sasuke. However, Sasuke summoned the snake Manda as a shield, and teleported both of them with a technique, at the cost of Manda's life. His team found him after seeing the explosion, and he went with them to rest, explaining what happened.

Brothers Meet Again
After seeing the explosion, Naruto's team heads to it, and Kiba tracks Sasuke's scent. Back with Team Snake, Sasuke asks what everyone found out about Itachi. Suigetsu and Karin found nothing, but Jugo communicated with the birds, who were able to sense Akatsuki's chakra coming out of their hideouts, which he marked on a map. They decide to go to the most recently used one to find Itachi. Meanwhile, Itachi heads to an Uchiha Hideout and sends two clones, one to find Naruto, and the other to find Sasuke. As Naruto's Team goes to find Sasuke, Karin can sense that they're coming, and informs Sasuke. Team Snake then leaves, and goes to the Akatsuki Hideout. Before that, Karin realizes that the team possesses scent trackers, so she asks Jugo to have the birds tear up one of Sasuke's shirts, which has a very strong amount of Sasuke's scent on it, and scatter the pieces to throw off Naruto's team. It does, and Kiba can no longer track Sasuke's scent. Naruto realizes that they need to split up, and Naruto finds Itachi's clone. Itachi claims he only wishes to talk, but Naruto knows he needs to catch Itachi. Naruto creates a Shadow Clone that attacks with a Great Ball Rasengan, but Itachi was a clone as well. The real Itchi catches Naruto in a Sharingan genjutsu. In the illusion, Itachi asks why Naruto cares for Sasuke so much, so Naruto claims that Sasuke's like a brother to him, and he's more of a brother to Sasuke than Itachi was. When Itachi goes on the offensive with his genjutsu, but Naruto dispels it. Itachi then dispels the clone, having run out of time to talk. The other clone encounters Sasuke at the Akatsuki Hideout. After a short greeting, Sasuke attacks the clone with his Chidori Current Blade, but Itachi substituted himself with a Shadow Clone as a shield. Sasuke is then caught in the clone's Sharingan genjutsu, but he easily dispels it. Itachi then destroys the clone, telling Sasuke to go to the nearby Uchiha Hidout so they can end their dispute. Sasuke and the rest of Team Snake to go to the hideout. Sasuke encounters two of Naruto's Shadow Clones, so he destroys them with Chidori Current punches, and the team continues on. Naruto figures out where Sasuke is, so Naruto's Team goes in pursuit of him. Unfortunately, Naruto's Team encounters Tobi. Naruto attempts two Great Ball Rasengans with Shadow Clones, but the attacks are absorbed by Tobi. Naruto's Team then prepares to finish Tobi off. Mean while, Sasuke encounters Kisame, who asks Sasuke to continue on by himself, since Itachi doesn't want interferences. Sasuke has no argument, and leaves his team with Kisame. Suigetsu and Kisame then prepare to fight for the Samehada. Sasuke then goes to the hideout and prepares to battle Itachi.

Infiltration of the Rain Village
Jiraiya tells Tsunade that he is going to, personally, gather information regarding the Akatsuki in the most probable place: the Rain Village. Seconds after Jiraiya sucessfully enters the village, he was detected by silent security set up by Pain. Konan was quickly dispatched to locate Jiraiya's location.

Jiraiya vs Pain
Jiraiya kidnaps two ninja's from the rain village and learns about the power of Pain. Konan locates Jiraiya and informs Pain who has changed bodies in a secret chamber. Konan then goes ahead and attacks Jiraiya, fighting evenly matched with him for a short time, and Jiraiya then tells about his past with Konan, Yahiko and Nagato. Pain then shows up and attacks Jiraiya. Pain then tells us he wants all to suffer like he did as a child so they will stop fighting and mature like he did. After a little while, Jiraiya enters Sage Mode and summons two toads. Pain then summons two of his other bodies and launch an evenly matched fight with Jiraiya. Due to pity for whom he believes is his former student, he lowers his guard and Pain launches a counterattack which severs Jiraiya's arm. Jiraiya has a flash back to when he met the Toad Sage who told him that he would be a pervert, he would travel the world, he would write a book and he would train the destined child who would either save or destroy the world. He believes this to be Pain. During the fight, Jiraiya learns Pain's secret (although it's not revealed) and his throat is cut. As he lay dying he has a flashback of a conversation he had with Minato and Kushina (Naruto's parents) and they want to name their son after the charecter in his book, there by making him Naruto's godfather. Remembering this, he forces himself back to life and writes a message on Pa's back. He says he now believes that Naruto is the destined child and it's up to him to decide his future. He then drifts off to his death.

Sasuke vs Itachi
Sasuke arrives at the Uchiha hideout and confronts Itachi. The battle begins with both of them using Taijutsu, Itachi with a kunai and Sasuke with his sword. Itachi grabs Sasuke's cloak and throws him, Sasuke loses his sword. Sasuke recovers and unleashes a Chidori. He runs towards Itachi, but only far enough to get to his sword at which point he punches the Chidori to the ground and runs his Chidori Current through the floor towards Itachi. Itachi leaps into the air, but before he realizes it, Sasuke stabs him through the chest with his sword. They fall to the ground and Itachi tells him that he has gotten stronger. Sasuke says that this is the end and before he kills him he has one question. Itachi then points towards the throne-like chair in the room where another Itachi sits. The stabbed Itachi disperses into crows and then the other Itachi says, "the end is a long way off, but I'm willing to listen, what do you want to know". Then Sasuke asks "have you gone deaf?", then a sword stabs through the back of the chair and through Itachi. Sasuke was behind the chair. The other Sasuke disperses into snakes and Itachi realizes it was Genjutsu. Sasuke then says, "I said this is the end and before I kill you, I have one last question." Sasuke asks "Who is he"? Sasuke recalls when Itachi said that three of the Uchiha clan would have the ability to use the Mangekyou Sharingan including himself if Sasuke would be able to awaken his. Itachi explains that the person who assisted him when he murdered the entire clan was none other that Madara Uchiha, one of the founders of Konoha. Sasuke does not believe him and continues to question him. Itachi reveals that one of the purposes of the Mangekyou Sharingan is to control the Nine-Tailed Demon Fox. He also reveals that once the Mangekyou Sharingan is activated, the more that it is used, it will progressively lead to blindness. Itachi refers to Madara (Tobi, leader of Akatsuki) as his mentor. The stabbing and the battle so far has all been Genjutsu and Itachi is finally activating his Mangekyou Sharingan. Itachi reveals that use of the Mangekyou Sharingan will slowly deteriorate the user's eyesight, and the only way to stop this is to take the eyes of another Sharingan user; he states that this is the reason he left Sasuke alive, and why he pushed him to become stronger. After a flashback of his childhood, Sasuke states "Finally... it all ends here."

As Itachi comes over to Sasuke, he rips out his left eye. In agony, Sasuke cries out, and as Itachi comes over to take the right eye, Sasuke assumes his cursed seal level one form. As he is held by an Itachi clone, the real Itachi comes over to take out the eye, when Sasuke activates his level 2 form. As Sasuke's eye is being ripped out, he wakes up. Itachi was using the Tsukyomi which Sasuke had overcome. Sasuke shortly lectured Itachi about the tools of the ninja, and how a tool is only as powerful as the ninja who uses it. Itachi tells Sasuke that he will make his dream, of ripping out the eyes, a reality, as he speaks of the other Mangekyou Sharingan jutsu. Zetsu speaks of his excitement to see it, as Itachi readies the Amaterasu. His eyes bleed. Itachi and Sasuke both use the Great Fireball Jutsu, and Sasuke holds a slight advantage until Itachi uses Amaterasu. The black flame burns out Sasuke's fireball and Sasuke runs. Everything Itachi sees is burned, but Sasuke evades it. Itachi uses another Amaterasu and it appears to have hit Sasuke, immediately melting through his remaining Curse Seal Level 2 wing and scorching his body. Itachi prepares to rip the eyes out of the half burned Sasuke, but Sasuke's body collapses as soon as Itachi approaches it; the corpse is shown to be an empty shell left behind by Orochimaru's Kawamari (Shedding Skin) Jutsu, and the real Sasuke has dropped below back into the shrine. He uses a new ninjutsu technique, named Katon: Gouoryuka no Jutsu (Fire Release: Grand Dragon Fire) from down below. Itachi dodges, but it still burns his arm. Soon it begins to rain, and Sasuke says that this new jutsu is unavoidable. Meanwhile Zetsu stares in awe.

Sasuke charges his final technique, Kirin. A huge creature made of lightning appears; the Grand Dragon Fire technique had dumped a huge amount of residual heat into the upper atmosphere and Sasuke's chakra remained suspended in a usable form, changing with the atmosphere from simply fire chakra into a bolt of lightning characterized in the same form as the earlier Grand Dragon Fire technique, but cast instead from lightning. Sasuke hits Itachi and Itachi appears to be dead. Itachi is then shown to be alive somehow and Sasuke goes into State 2. Itachi then reveals a third Mangekyou technique: Susanoo. Susanoo pulls a sword out called the Sakenagi Longsword. Giant snakes appear out of Sasuke. The snakes attack and Orochimaru appears inside the mouth of one of the snakes. Sasuke, having used up nearly all of his chakra fighting Itachi, could no longer supress Orochimaru, who has been inside of Sasuke since his failed attempt at taking over his body. The snakes are all killed but the last one spews up Orochimaru, Orochimaru is stabbed by the Sakenagi, sealing him in an eternal dream state, his remains (as well as the remains of the snake) are subsequently sucked into the Sake jar that the Sakenagi Longsword in sheathed in. Itachi then asks Sasuke if that's all he has. Sasuke then proceeds to attack Itachi again, first throwing kunai knives at him, then using summoned paper bombs and a sword. However, each of these attacks is reflected by another effect of Susanoo, Yata's Mirror, which reflects all attacks directed at Itachi. Sasuke is knocked back by his own attacks and lies on the ground. Itachi seems to be invincible when the Susanoo jutsu begins to fade and Itachi walks toward his brother seeking his eyes. When Itachi reaches Sasuke he places his blood stained hands on his face but suddenly falls to the ground. Zetsu figures that Itachi must have been injured before the battle started, also noting that Itachi was unable to dodge attacks he would normally be able to. Sasuke then smiles and closes his eyes before collapsing himself, as Itachi's Amaterasu continues to burn around them.

Meanwhile, Naruto and the other members of the 8-man squad continue to fight Tobi. Shino attacks with his bugs and even manages to completely swarm Tobi with them. Tobi escapes from the swarm unharmed and Zetsu arrives to tell him that Sasuke won the battle and that Itachi is dead. This was no surprise to Tobi. Zetsu also says that Sasuke is probably dying as well. Just before Tobi and Zetsu leave, Kakashi notices Tobi's Sharingan. Kakashi states this, while Tobi and Zetsu flee to the battle-site. Hinata sees storm-clouds and the flames of Amaterasu with her Byakugan. Naruto and the group pursue them. Meanwhile Tobi and Zetsu reach Sasuke. Tobi tells Zetsu to take Itachi's corpse. Naruto's team reaches the flames, and Yamato uses Earth Style: Winding Fissure to create a path through it. Naruto becomes angry when he realizes that they were too late.

Truth About The Uchiha Clan
Sasuke wakes up in a large room. Tobi appears from the shadows and says he will tell Sasuke "the truth" of Itachi. He then begins to take off his mask. As Madara's Sharingan is shown, Sasuke's Sharingan is turned into Mangekyou. His eyes bleed and Amaterasu appears around Tobi. Tobi says that Itachi implanted his abilities into Sasuke, and that they would activate as soon as Madara's Sharingan is shown. Madara then says that Itachi did this to kill Madara, and protect Sasuke. Sasuke doesn't believe him and yells at Tobi to go away. Tobi then begins to tell Sasuke the secret, about how Itachi tried to protect the village and Sasuke. Itachi was ordered by the elders of Konoha to annihilate the Uchihas because they were planning a coup d'état against Konoha. Itachi did this because he detested war and wanted to maintain Konoha's stability. Madara also tells Sasuke the history of Konoha and the Uchihas. This triggers a flashback to moments before itachi's death; revealing that he was not seekings his brothers eyes but in his final stance with sasuke poking him on the head (as he did in sasuke's childhood) and smiling at him. After this Sasuke is shown joining back up with Snake with his new Mangekyo Sharingan. He tells the group that they will be called "Hawk" from now on, and their goal is "the complete and utter destruction of Konoha."

Sasuke's Revenge arc

 * This arc covers chapters 403-Present.

Decoding the Message
Naruto sits in his room and flashes back to his meeting with Itachi in the forest, just before his death. Itachi and Naruto talk about Naruto's fascination with his younger brother, Sasuke. Itachi wants to know what Naruto would do if Sasuke would ever attack the village and Naruto shrugs it off as impossible. Itachi insists and Naruto says that he would protect the village without killing Sasuke. Itachi then gives Naruto some of his power and tells him that he hopes that he will never have to use it. Meanwhile Sasuke and Madara are talking about what to do with Itachi's eyes and Sasuke refuses them. Sasuke also reiterates his desire to restore his clan and says that he will do it "my own way".

Back in Konoha, Kakashi tells Naruto to meet Tsunade at her office. Naruto does so, and he is greeted by Pa. Pa tells him Jiraiya was killed in battle. Meanwhile Hawk and Akatsuki join forces, and will capture the last 2 remaining tailed beasts before they attack Konoha. In Konoha Pa shows the coded message that Jiraiya wrote on his back before he died. Naruto leaves the room furious and later enters a depression, but is soon cheered up by Iruka. Meanwhile, Tsunade asks Shikamaru to decode Pa's message, and puts him in charge. She leaves the room, and begins to cry. Jiraiya sends a toad to Ibika Morino with a prisoner from Hidden Rain Village for interrogation later. Meanwhile Shikamaru had the decoding team decode the message. The team says that without the key, they would have a hard time decoding the message, and suggests that Shikamaru go to either Kakashi, the 5th Hokage or Naruto because they may have been heard Jiraiya say something pertaining to the message. The 5th doesn't remember anything, all Kakashi heard is Jiraiya discussing the size of Tsunade's particularly huge breasts and Naruto is sad and nothing else. Realizing that the operation is useless, Shikamaru leads him to the hospital, where Kurenai is staying. Naruto was surprised that Kurenai is pregnant. Kurenai wished that Shikamaru would no longer visit her, but Shikamaru says that he promised Asuma that he would. Shikamaru then tells Naruto that the baby would become his apprentice. Then he said that he wanted to be as cool as Asuma and Jiraiya too, and now they must not be kids anymore, and that they are not in that position anymore. That they must be the ones entrusting, not the ones entrusted. In the meantime they try to decode the message. Naruto finds it strange that there is only one character in the katakana script. They figure out that Jiraiya has written his code from the book he is writing when he is with Naruto. The message means, "The real one isn't there". They then decide to talk to Fukasaku, who fought Pain.

Fukasaku's Training
Meanwhile Akatsuki decides what course of action to take. Madara says that Pain must capture the nine-tailed beast before Konoha decides what course to take and Sasuke will deal with the eight tailed beast. Pain asks if Sasuke can complete the task, Madara says he is confident that Sasuke can do it. Pain then tells Konan to get ready, revealing his new sixth body, which is a female. All prepare to go to Konoha to take the Nine Tailed fox. After trying to assist Shikamaru in deciphering Jiraiya's code, Naruto was adamant on destroying Pain. Pa (Fukasaku) offered to train Naruto in Senjutsu, seeing as Naruto stood no chance of killing the apparent Akatsuki leader. Naruto readily accepted his offer and is brought to Myobokuzan with a reverse summoning Jutsu where he is taught the difference between Ninja Techniques and Sage Techniques through natural energy. In order to help Naruto gather natural energy, Fukasaku smears some Secret Frog Oil on Naruto's skin, however it begins turning Naruto into a toad but he is shocked back by being whacked by Fukasaku; it is then revealed that those who can't control the natural energy are turned into Toads and that the statues of Toads are all past ninja who were turned into toads, Naruto decides to do the training anyway. Naruto perfects the Senjutsu training with the Secret Frog Oil and mentions a jutsu he can finally perfect. Fukasaku gives Naruto Jiraiya's first book, The Legend of the Gutsy Ninja, before continuing with his Senjutsu training without the Secret Frog Oil. Naruto begins gathering natural energy without the oil, but starts turning into a toad. Fukasaku says he's not concentrating hard enough, reminding him he mustn't move. When Naruto suggests taking the oil with him in battle instead of learning how to draw natural energy without it, Fukasaku dismisses the idea, revealing that out of Myobokuzan's atmosphere, the oil evaporates quickly. He then takes Naruto to some peak formations, where Naruto must stay utterly still in order to maintain equilibrium not to fall down, as well as to take in the natural energy without turning into a toad. When he starts to fall, Fukasaku saves him from falling with his tongue. After some training Naruto masters the way to harness the natural energy and as a result he is  able to enter Hermit Mode.Fukasaku is really impressed by his progress even saying that Naruto has become a better hermit than Jiraiya himself since after entering Hermit Mode he now has no sign of frog transformation on him. Instead he has around his eyes some kind of black circles which according to Fukasaku are the signs of a true hermit. After finally completing the natural energy training ,Fukasaku tells Naruto that now with the natural energy he has accumulated he will learn the "kawazu kumite," the frog martial art.That night Naruto  begins to form his technique in secret, while Fukasaku isn't looking saying that he still needs more time in Hermit Mode to perfect it. Later Pa tells Naruto that Sage Mode has a weakness. Those who use it must stay still while aquiring Natural Energy, thus leaving them open to attack. Naruto is at first angry that he has wasted his time but Pa assures him that in order to overcome this weakness they must merge, with Pa stuck to Naruto's shoulder. He says that by this method Pa could stay still and aquire Natual Energy while Naruto could move and use it. He further explains that this was how Jiraya fought against Pain, with Ma and Pa stuck to his shoulders.

In the background, Naruto is shown lying around as Fukasaku comes around and asks him where he keeps disappearing, unaware of Naruto's secret technique preparation. Naruto evades the answer by replying that he is just trying to relax.

Fukasaku tells him to come down as it is time for them to practice toad fusion. Naruto absent mindedly remarks whether Konoha is all right or not. As Fukasaku looks at him surprised, Naruto states that since Akatsuki are looking for him they might actually attack Konoha. Fukasaku scolds him saying that he is dumb, and that there is no need for him to worry as Konoha has a huge number of excellent ninja, and if anything was truly wrong, they would have sent a messenger frog to warn them. Naruto relaxes and they both leave to train.

Eight-Tailed Beast
Sasuke and Hawk have managed to find the location of the eight tailed beasts host by interrogating it out of another Cloud nin through Sasuke's Mangekyo Sharigan; the Cloud nin reveals that the host is training in Unraikyo, and also describes him as carrying a seven bladed sword. Meanwhile, a large kraken like monster is sucked back into the shadow of a man who later appears from a tent, remarking that the sun is in his eyes. Later Sasuke and Hawk eventually confront the eight tailed host; Kirābī. Kirābī easily fends of attacks from both Suigetsu and Jugo. He easily knocks out Jugo, and Sasuke prepares to battle him. Sasuke engages Kirābī in a sword fight which ends in a draw, Kirābī then decides to fight more seriously and shows his seven sword style. With this fighting technique, Kirābī utterly dominates Sasuke, even mimicking Sasuke's Chidori Current, and impales Sasuke with all seven of his swords. Just before he kills Sasuke he is blocked by Jugo and Suigetsu while Karin heals Sasuke by letting him suck her chakra. Once Sasuke joins the fight again, Kirābī is struck by an enlarged fist by Jugo while also struck by a Chidori from Sasuke. Kirābī retreats while muttering that the "weaklings" are more annoying then he thought, he then decides to power up in a fashion similar to Naruto and attacks Sasuke then Sasuke's team. Sasuke attempts to use his Mangekyo Sharingan to trap Kirābī in a genjutsu only for him to break out of it with help from his Tailed beast and fatally injures Sasuke. While Jugo tries to heal Sasuke, Kirābī, finally tired of toying with them, unleashes his full power and transforms into his full tailed beast state and prepares to destroy them. Suigetsu creates a giant wave of water to hold him off so the others can get away, but is blown unconscious from a powerful chakra beam. Sasuke, out of desperation uses Amaterasu to try and stop Kirābī. Sasuke succeeds and uses Chidori Blade to cut the Tailed Beast's tentacles. While the Tailed beast is trying to get rid of Amaterasu's black flames, it hits Karin, igniting her. Sasuke is able to use his own Mangekyou Sharingan to put out the flames, both hers and Kirābī's, who has returned to his human form. Juugo grabs Karin and Kirābī and they begin to move out. The two ninja watching learn that there is someone from the Uchicha clan and goes to warn the Raikage. The Raikage is furious. Meanwhile, Sasuke brings the body of Kirābī to Madara. While Sasuke heals his wounds, Madara goes to the sealing statue, meeting Kisame and Zetsu stating that they have to wait for Pain to get back from retrieving Naruto. While Hawk heals their wounds, Suigetsu asks Sasuke if he still wants to take the 8-tails' power, but Sasuke says he now has power enough to destroy Konoha, but accidently spills a cup of water, hinting that his eyesight is deteriorating. Suddenly Karin senses that someone is spying on their base. Jay, the Kumogakure spy, tries to send a message lizard, but then Sasuke pierces it with his sword revealing himself to Jei. When the Raikage finds out that his messages stop, he decides to send a team of ninja to find Akatsuki and retrieve his brother, while he sends a message to the other kage for an inter-country meeting.

Back at the sealing statue, Kirābī's "corpse" suddenly turns into one of the Eight Tails' tentacles mid-sealing. Madara realizes that Sasuke has failed in his mission.

Back where Kirābī and Sasuke fought, Kirābī climbs out of one of the tentacles that Sasuke had cut off mid-fight. He reveals to the Eight Tails, who he converses with casually, that he intentionally pretended to lose to Sasuke, just so he could go on a vacation, away from protecting his village. The Eight Tails comments that he feels a new era in the ninja world is approaching.

Pain's Assault on Konoha
Pain and Konan arrive in the outskirts of Konoha after defeating a group of ninjas. Pain then divided his six bodies into two groups: distraction and reconnaissance. Konan is on reconnaissance as well. Pain then used his Rinnegan to see the barrier around Konoha and sent in one of his bodies, Animal Realm. This body tricked Konoha into believing that there was only one intruder. Animal Realm summons the other bodies and Konan into Konoha then began invading Konoha. Buildings were attacked, and attacks on other ninjas were done for information on the Nine-Tails by Pain's bodies. Konoha detected the invasion and sent a small team of ninjas to encounter the intruder(s). Iruka tried to help a fallen ninja, but then God Realm Pain arrived. He was about to attack Iruka for information on Naruto, but Kakashi stepped in and began to fight Pain. Pain attempted to kick him but Kakashi kicked summoned a wall. Pain then impaled Kakashi's shoulder with his spear-like weapon but Kakashi held on to it to keep Pain in place, he tried lighting blade but he somehow missed. Pain used a technique to blow Kakashi away while destroying the surrounding area. Kakashi pondered the attack and tested Pain's defenses by using a long range lighning justu that was shaped like wolf, but it had no effect on him. The Code Breakers managed to break into the body of Pain Jiraiya, sent to Konoha for examination. They discovered that the piercings in Pain's bodies acted as chakra receivers, which might be the secret of Pain's powers. Demon Realm Pain then shot a missile from its head and destroyed multiple buildings. Soon after, Demon Realm returned to God Realm's location, surrounding Kakashi.

Tsunade was told of the attack and sounded the emergency alarm. She also issued an order to call back Naruto. But the elders did not want Tsunade to call for Naruto stating that Naruto was safer where he was and Konoha would be in danger if Akatsuki got a hold of Naruto. Tsunade grabbed the elders by the collar and told them that Naruto had the will of fire, so he has to protect Konoha. She said that, unlike Sarutobi, Jiraiya, and Chiyo, they have no faith in the next generation. They then got up off the ground, told her to do as she wished, and left. Tsunade, Shizune, and the elders went to find out more about Pain. When the toad was ready to go to call back Naruto, Danzo kills the toad with a sword in order to keep Naruto away from Pain. In the background, Naruto is shown panting in front of a widely destroyed area. Apparently, Naruto has finished his new hidden technique and it is so powerful that it is capable of destroying three complete mountains at the same time. Meanwhile Konan has silently been interrogating shinobi and civilians alike in the city trying to find out Naruto's whereabouts. She is shown subjugating a unknown shinobi whose face is not shown. The man absolutely refuses to cave in and insults Konan. She, in a fit of anger, kills him instantly by crushing his head with her Origami Technique which kills the man instantly by obliterating the man's head.

Kakashi vs Pain
Kakashi realizes the way Pain works by recalling Fukasaku's warnings. However, he realizes that without heavy backup, he is no match for Pain, as facing Pain single handed is nothing short of suicide. Meanwhile Tsunade summons Katsyui to heal everyone injured at the cost of her chakra declaring that she would fulfill the oath of the Hokages. At the battlefield, Kakashi tries to escape from Pain desperately so that he can warn others about the only way Pain can possibly be defeated. Meanwhile Demon Realm Pain morphs into a chameleon like figure with a huge sword tail, similar to Sasori's puppet Hiruko. He then stabs Kakashi right through the heart, only to be surprised as it is revealed to be a lightning clone, which electrocutes Demon Realm Pain. Before Pain can react, Chouza Akimichi and Choji, his son, both in their giant size crash down upon Demon realm Pain, apparently crushing him as numerous ninjas come with them to aid Kakashi, who finally relaxes as reinforcements have finally arrived.

Pain's first body observes everything calmly and prepares to enter battle as the horde of shinobi now look at him.

As Choza and Choji come to his assistance, God Realm Pain (Yahiko) calmly steps in analyzing everything. Kakashi explains to Chouza that he used a Raikage Bunshin : Lightning Clone Technique to escape Pain, and although successful, it has taken nearly half of his chakra.

As the Konoha shinobi who have arrived try to attack Pein from all sides, Pain calmly invokes a technique called Shinra Tensei and instantly a massive explosion occurs in the area which destroys all the surrounding buildings, as Chouza and Kakashi manage to deflect the debris, Kakashi uses the opportunity to throw a kunai with a exploding bomb at Pein who calmly deflects it aside without even apparently noticing it.

Chouza is surprised at this and looks at Kakashi for an explanation. Kakashi quietly explains to his colleagues that Pain has the ability to control gravity and therefore has the ability to both propel and repel attacks as the situation calls for it. He then tells everyone that although Pain has that ability, he apparently can't use it in succession and there is a small interval of time before he can use the technique again.Everyone comes to the conclusion that although an interval exists it is too small to be exploited. As everybody wonders what to do, Kakashi speaks up.

Kakashi tells everyone that he has a plan and requires their assistance. He then tries to attack Pain from underground exactly in the way Naruto did to defeat Neji in the Chunin exam finals. Pain again uses his gravity technique and flings Kakashi away. Pain calmly remarks that Kakashi is extremely skilled and leaving someone like him alive would cause a lot of trouble to him in the long run.

In the meanwhile Kakashi yells at the Akimichi's, who try to attack Pain from both sides using their Spiked MeatTank Attack. Pain calmly flings both Chouza and Choji aside remarking they are too slow and predictable. As they are being flung away, the two Akimichi's suddenly yank upon a chain which appears from underground and binds Pain tightly restricting his arms and preventing him from using his gravity technique.

Pain realizes that Kakashi had already planted the chain underground before he came forward to face him and commends Kakashi's skill. Realizing his chance, Kakashi charges his Raikiri at full power and charges at Pain. However, suddenly Demon Realm Pain jumps in front of him and takes the attack head on. The Raikiri apparently destroys Demon Realm, but does not kill him. Everybody else is shocked at the thought that more than one Pain can move at the same time, especially Demon Realm who they thought was already destroyed.

Kakashi looks on in desperation as everything around him lays destroyed. Both Akimichi's are laying unconscious and injured and the other shinobi who arrived with them lying apparently dead.

Kakashi himself is severely injured and is unable to move. Pain casually remarks that the Kakashi in front of him is not a clone, apparently taunting him, and remarks that Kakashi can no longer move. Meanwhile from a fallen wooden board, a nail floats up brought out by Pain's skills. Pain remarks that it is time for Kakashi to die, and speaks out saying he will stay at a distance from Kakashi, just in case. He ends the talk saying it is time for Kakashi to know pain, and Kakashi realizes that he cannot dodge and glares at him in defiance; as Pain calmly stares at Kakashi and repels the nail with full force at Kakashi. In the end Kakashi is shown flinching as specks of blood fly out in the air. It is not shown whether Kakashi has been killed or if he has just been seriously injured.

Kakashi survives. Choza died in the attack protecting his son. Kakashi tells Chouji to go and tell Tsunade of Pain's power. Then Demon Realm Pain sends another flying missile aimed at Chouji. Kakashi uses his Mangekyou Sharigan to send the missile to another dimension, knowing that if he does so, he will be out of chakra and that he will die.

Danzo's Treason
Danzo killed the messenger frog that was to be sent to Naruto and Fukasaku to report on Pain's assault. Danzo does not want Naruto to fall into Akatsuki's hands. He hides with his ANBU in an underground tunnel, waiting for the commotion to end above. He mentions that his plan is to become Hokage by removing Tsunade.