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 began last January 2008, in the US issue of Shonen Jump.

The new story revolves mainly around Naruto Uzumaki and Sakura Haruno's new adventures and their search for Sasuke Uchiha after he defected from 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.

Senjutsu Training arc

 * This arc covers chapters 403-418.

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 Taka 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. The toad that Jiraiya sent reaches Ibiki 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 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 was 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 staff; 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 Sage Mode. Fukasaku is really impressed by his progress even saying that Naruto has become a better sage than Jiraiya himself since after entering Sage 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 sage. 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 Sage 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 acquire Natural Energy while Naruto could move and use it. He further explains that this was how Jiraiya 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.

Fukasaku and Naruto begin to practice Toad Fusion. Fukasaku keeps getting thrown off because apparently the Nine-Tailed Fox rejects him. It seems that the Sage Training was for naught. Naruto then decides on undertaking the impossible task of using Sage Mode while moving remembering the fact that Jiraiya's last message to Naruto was not to give up. Naruto kept on attempting to run while gathering Natural energy, but couldn't maintain it. Fukasaku then said that to do it, you'd have to look both left and right at the same time. After hearing that, Naruto recalled that moment when Kakashi said that.

Naruto and Fukasaku was told by a unnamed toad that the messenger toad's name had gone missing from the tubes, and is also told by Shima, who is nearby Konoha, that something is happening. Naruto, Shima, and Fukasaku are planning on summoning something big, something apparently only all three of them can summon by working together.

Sasuke & The Eight-Tailed Beast

 * This arc covers chapters 410-417.

Meanwhile, Sasuke and Taka have managed to find the location of the eight tailed beasts host by interrogating it out of another Cloud nin through Sasuke's Mangekyo Sharingan; 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 Taka eventually confront the eight tailed host; Kirābī. Kirābī easily fends off 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 sharp spear to cut the Tailed Beast's tentacles. While the Tailed beast had tried to get rid of Amaterasu's black flames, it hit Karin, igniting her. Sasuke was able to use his own Mangekyo Sharingan to put out the black flames, both hers and Kirābī's, who returned to his human form. Jugo grabbed Karin and Kirābī and they begin to move out. The two ninja watching had learned that there had been someone from the Uchiha clan and went to warn the Raikage. The Raikage was furious. Meanwhile, Sasuke brought the body of Kirābī to Madara. While Sasuke was healing his wounds, Madara went to the sealing statue, meeting Kisame and Zetsu and stating that they had to wait for Pain to get back from retrieving Naruto. While Taka were healing their wounds, Suigetsu asked Sasuke if he still wanted to take the 8-tails' power, but Sasuke said he had enough power to destroy Konoha, but accidentally spilled a cup of water, hinting that his eyesight was deteriorating. Suddenly Karin sensed that someone had been spying on their base. Jei, the Kumogakure spy, tried to send a message lizard, but then Sasuke pierced it with his sword, revealing himself to Jei. When the Raikage had found out that his messages had been stopped, he decided to send a team of ninja to find the Akatsuki and retrieve his brother, while he sent a message to the other kage for an inter-country meeting.

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

Back where Kirābī and Sasuke fought, Kirābī climbed out of one of the tentacles that Sasuke had cut off mid-fight. He revealed to the Eight Tails, with whom he conversated 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 commented that he had felt a new era in the ninja world is approaching, which Kirābī took to mean a new career in music for him.

Invasion of Pain arc

 * This arc covers chapters 419-449.

Initial Attack
Upon reaching Konoha, Pain discussed the battle plans for the invasion. The Animal path, Asura path, and Preta path will act as diversions while the Deva path, Naraka path, Human path, and Konan interrogated villagers on the whereabouts of Naruto Uzumaki, the Jinchūriki of the Nine-Tailed Demon Fox either through mind reading or threat of death. Once preparations were complete, the Asura path threw the Animal path into the village where it summoned the other Six Paths of Pain and the invasion began.

Because Konoha only expected one invader, the multiple points of attack made it difficult for Konoha react. The Fifth Hokage called for Naruto to return to the village to aid in its defense, but the messenger toad Kosuke was killed by Danzo before he could leave, to prevent Akatsuki a chance at capturing the demon fox. Meanwhile Tsunade remained at the Hokage Residence to summon and use Katsuyu to heal any villager who was injured during the attack.

Kakashi Hatake engaged the Deva path, who was quickly backed up by the Asura path. Choza and Choji Akimichi came to Kakashi's aid and discovered the Deva path's unique gravity manipulation has a five second window. Despite discovering this secret and the Asura path defeated, Choza was critically wounded and Kakashi incapacitated, leaving only Choji to deliver the information to Tsunade. Konohamaru Sarutobi engaged and defeated the Naraka path, while Tsume and Kiba Inuzuka engaged the Preta path.

As the Deva path confronted Tsunade to question her about Naruto, Shizune, Inoichi and Ino Yamanaka discovered the secret of Pain's Six Paths. The chakra receivers planted in the body of the body Jiraiya sent back revealed that each body is merely a animated corpse powered by chakra, and that Pain's real body is else where. As Shizune summarized their analysis, the Human path found and read her mind discovering Naruto was at Myobokuzan. Upon finding out and angered by Tsunade's precieved lack of pain, the Deva path recalled Konan and the other five Paths out of the village where he detonated a powerful Shinra Tensei, destroying most of the village.

Counterattack
Having caught word of Pain's attack, the toads at Myobokuzan prepared for the counter attack. Shima, who was at Konoha at the time was told to prepare a reverse summoning to bring Naruto Fukasaku, Gamabunta, Gamaken, Gamahiro, and Gamakichi to Konoha, moments after the Shinra Tensei leveled the village. After using the Naraka path to repair the destroyed Asura path, the Animal was launched back into the village and re-summoned the rest of the paths back into the village to fight the Jinchūriki.

Using his newly learned senjutsu techniques and a perfected Wind Release: Rasenshuriken, Naruto defeated the Asura, the Human, the Animal, and the Naraka path before the Deva path regained enough strength to fight on it's own again. When he was finally caught and held by the energy absorbing Preta path, Naruto used the senjutsu chakra to disrupt the Preta path's chakra flow turning it into a frog statue before finally facing the Deva path, Pain's last and most used body. Pain quickly dispatched the giant toads and gained the upper hand, killing Fukasaku in the process. Using another gravity manipulation jutsu to grab and stabbed him to the ground with his Chakra Disruption Blades to take him away. Before departing, Naruto asks Pain why he has done everything, to which Pain replies that the world can never have the peace Jiraiya fought for because the world was to full of hatred, and therefore the only way to create world peace is through force. By using the Tailed beasts, Pain planned on making a weapon strong enough to destroy a country, and the fear of that weapon will prevent more fighting.

Shikamaru Nara, having survived the destruction of Konoha, met with the Yamanaka group carrying Shizune's body. When they are told what information she knew, Shikamaru concluded that Pain's real body was somewhere close to the village, at a high enough place that he could send his chakra across a large enough distance to control the Six Paths with no difficulty. As Pain is describing his quest for world peace, his true body, Nagato, emaciated with several chakra blades sticking out of his back in his and Konan's hiding place, a makeshift tree on a high mountain close to the village. Hinata Hyuga came to his rescue, confessing her love for Naruto, but was then quickly struck down and critically wounded. Believing her killed, Naruto lost control of his anger and slipped into his six-tailed transformation. With the demon fox in control of Naruto's body, it fought Pain causing him to retreat from the village to get close enough to Nagato to use Chibaku Tensei. With the demon fox controlling Naruto and Pain out of the village, Sakura Haruno ordered all who can help to tend to the wounded and for a team, including herself, to help the critically wounded Hinata. Team Guy, who was returning from a mission passed the injured Gamabunta who informed them that Konoha was in danger. Elsewhere, Yamato, who was with Sai, and Anko Mitarashi on a mission hunting Kabuto Yakushi, senses that Naruto has released six-tails of the demon fox and heads back to find and stop Naruto.

While still being presued by the demon fox, Pain, through great strain of Nagato, uses the Chibaku Tensei to create a giant miniature moon in an attempt to capture the demon fox. During this time, Naruto locked in his own subconscious and lost in despair calls out for help to a response of Pain's visions of peace. In the end, while evil Pain had a plan to deal with the hatred in the world, Naruto did not. Taking advantage of his pain, the demon fox convinced Naruto to destroy everything in the world by releasing the seal. This causes the seal to distort. Despite the strength of the miniature moon, the distorted seal allowed the eighth-tail to grow, partially breaking free of the sphere.

In his mind, just as he was about to remove the seal to release the ninth tail, Minato Namikaze, the Fourth Hokage appeared and spoke with Naruto. Minato revealed to Naruto that he was his father, and he sealed the demon fox into him because he too felt that the demon fox was forced to come to Konoha and believed a masked being within Akatsuki was behind the attack. After easing Naruto's fears that he cannot change the world, Minato repaired the seal and sent Naruto back to finish his battle with Pain.

With the demon fox's chakra suppressed, Naruto and Pain resumed their battle, with Naruto tricking Pain into using a Shinra Tensei on dozens of shadow clones, giving Naruto enough time to strike him with a Rasengan during the five second window. The last body of Pain was defeated and Naruto used its chakra receivers to track down and confront Nagato himself.

Nagato
Having reached the makeshift tree, Naruto asked Nagato why he hated Konoha, and what made him the way he is. Nagato, still wanting to know Naruto's reply to his questions, answers with two stories. The first was how his parents were killed during the Second Great Shinobi World War, which lead to the activation of his Rinnegan eyes. The second, he began with how he met his friends Konan and Yahiko, the boy who's body would later become the Deva path. Yahiko revealed to the small family he wanted to rule the world to stop the worlds wars. After their dog, Tiny was killed by an exploding tag as collateral damage from the Sannin's battle with Salamander Hanzō, Yahiko declares he won't just rule the world but become a god, a dream that sparked a desire for the same from Nagato.

Nagato then revealed how Yahiko approached Jiraiya to ask him to train himself, Nagato and Konan to be ninjas. During the training, Nagato had used the Rinnegan to save Yahiko. Seeing this, Jiraiya told Nagato about the time of never-ending wars, a "messiah", the Sage of the Six Paths, appeared and spread his religion across the world, that came to be the ninja techniques that the shinobi use today. Jiraiya thought the Sage had been "reborn" as Nagato, and entrusted him to find the "answer" and spread peace in the world, before leaving the three orphans. Years later, the three formed a gang in Amegakure, lead by Yahiko, to abolish wars and bring peace in the world. Their fame captured the attention of Hanzo, who approached Yahiko to join hands and work together to bring peace among the war-torn countries of Earth, Fire and Wind. But this association turned out to be a trap laid by Hanzo, as he feared that Yahiko's group would take over the leadership of Amegakure. He lured Yahiko and Nagato to area which was surrounded by many Konoha ANBU Root shinobi, with Danzo leading them. Hanzo had kidnapped Konan, and then proposed for Yahiko to die to save Konan's life. He threw a kunai in Nagato's direction and ordered him to kill Yahiko. Yahiko agreed to die, but Nagato refused to kill him. Seeing this, Yahiko forcibly held Nagato's hand with the kunai and slit his own throat with it. A dying Yahiko told Nagato that he had to live as he was the "messiah". Nagato told Naruto that Yahiko's death was the second great source of pain for him. This incident led Nagato to go beserk, as he used his Rinnegan's abilities to subdue and backfire all attacks on him by Hanzo's men. But in the midst of all this, Nagato's legs were horribly burnt by Hanzo's Fire Release technique, while he was saving Konan. He ultimately summoned a large, animated statue for battle, which imbued several chakra rods from it's body into Nagato's back, to use the latter's chakra. The statue then released a soul removing dragon, that killed many of Hanzo's men, but as Nagato was about to target Hanzo himself, he fled the scene with the Body Flicker Technique. Nagato tells Naruto that he became the leader of their gang and carried on Yahiko's agenda to bring peace in the world.

After hearing Nagato's story, Naruto reflects on everything he's heard. Naruto agrees that some of the things Nagato mentioned are true, but he also said that Jiraiya believed in him and that he would believe in what Jiraiya believed in, and that's why he would not kill Nagato. Nagato questions this and Naruto pulls out the book that Jiraiya wrote.He begins reading it and tells Nagato the main character's name is Naruto. Naruto then says he WILL become Hokage and he promises peace for Amegakure as well. Nagato then states that Naruto was like him when he was younger. He says that he will believe in Naruto and gets ready to use a jutsu.

Upon using the jutsu Nagato uses the King of Hell statue to release all the souls that had been captured, and used it to also revive those who had died including Kakashi, Fukusaku and Shizune. At Myobokuzan the Great Toad Sage is telling Gamabunta that everyone has been revived and that he finds it surprising that it was two of Jiraiya's pupils that would bring about the revolution to the Ninja War. Nagato then entrusted his will to Naruto and passed away. Konan decides to leave and take both Nagato and Yahiko's bodies and tells Naruto that she will believe in him. She then uses her paper jutsu to create a bouquet of flowers and gives them to Naruto.

Meanwhile Sasuke and Taka prepare to move to Konoha.

Sasuke and Konoha arc

 * This arc starts from chapter 450.

Kakashi fetches Naruto and returns him to Konoha. Everyone has gathered to congratulate Naruto on his victory. Team Samui have now reached Konoha. Tsunade is now in a comatose state and is unresponsive, and as such, a new Hokage is to be elected. In the meeting to decide who the next Hokage would be, Shikaku nominates Kakashi, much to Danzo's annoyance. Danzo then says that all the previous Hokages have in some way destroyed the village. The Land of Fire Damyio then elects Danzo as the Sixth Hokage.

Meanwhile, Naruto meets up with Tazuna and Inari, of which they thank him for what he's done for them and return the favour by offering to help rebuild Konoha. However, Danzo has now ordered for Sasuke's elimination as a missing-nin. Elsewhere, Danzo summons Sai, whom he orders to watch Naruto. Sai, later, confronts Naruto and Sakura. They ask him about Danzo, and are furious at him when he replies that he can't tell them anything about Danzo. Shocked, Naruto and Sakura accuse him of taking sides with Danzo. Sai denies this and simply shows them his tongue, which has a seal on it. Sai reveals that all ANBU Foundation Members have this seal, which paralyzes them whenever they reveal something about Danzo.

Upon hearing them talk about Sasuke, Team Samui immediately assult them. When Naruto asks why they are attacking them, they begin by saying that they overheard them talking about Sasuke (that is, when Naruto tells Sai that Danzo wants Sasuke eliminated). Team Samui then tell Naruto that Sasuke Uchiha had attacked their village. Naruto wonders why Sasuke would do such a thing. Team Samui, confused, explain to Naruto that Sasuke is a member of Akatsuki, and that the Hokage has given them permission to kill him.