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.

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 its 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 whose 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 its 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, Fukasaku 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.

Summit of the Five Kage arc

 * This arc starts from chapter 450. to current

New Orders
Kakashi finds 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 Hokage have in some way destroyed the village. The Fire Daimyo then elects Danzo as the Sixth Hokage.

Meanwhile, Team Kakashi met with the employers of their first major assignment, Tazuna and Inari who have agreed to help rebuild Konoha. Elsewhere, Sai is assigned by Danzo to watch Naruto, and report his actions back to him. While Team Kakashia and Tazuna discuss Sasuke, and Naruto tells his friends he still intends to save Sasuke, just as he receives the order to eliminate Sasuke as a missing-nin. Upon returning, Sai remarks he is unable to reveal Danzo's reasoning because of cursed seal given to all ROOT members.

Over hearing information about Sasuke, the two members of Team Samui, Omoi, and Karui attack Team Kakashi for information about Sasuke and Akatsuki Knowing Akatsuki's goals, Naruto offered his support in finding Killer Bee and rescuing him before the extraction. They take Naruto to a secluded area, unknownst to them are followed by Sai, and interrogate Naruto. Naruto however due to the lessons he learned from Pain, offers himself to be beaten to relieve Karui of the pain she felt. After a through beating, Sai steped in to protect Naruto and Omoi himself stated that no matter what Karui did to him, he will not betray Sasuke. Samui finds them informs them that they will be going to the Raikage to give them their report.

Taken for medical care, Naruto tells Kakahsi, Yamato, and Sai his intentions to leave the village and find the Raikage and ask for a pardon for Sasuke. Yamato reminds him however that without the First Hokage's Necklace, the already weak seal shouldn't be strained, and as he was assigned to help rebuild the village, couldn't be there to seal the Nine-Tails. Naruto told them that his father told about the one in the mask that is controlling the members of Akatsuki, the attack on Konoha and was strong enough that Minato couldn't defeat. When pressed for anything else the Fourth told Naruto, Naruto tells him that he believed in him, which was enough to convince Kakashi that Yamato and himself would accompany Naruto to the Raikage.

Taka's Move
As Taka, after abandoning Akatsuki ater the completion of their goal to capture the Eight-Tailed Giant Ox are stopped by Madara Uchiha, who is angered at Taka's failure of catching the Eight-Tails and betraying Akatsuki. When Sasuke attempts to fight his way through, Madara says he will fight Sasuke, and then calmly tells him that Konoha was already destroyed by Pain and he gives him a new assignment, to kill the new Hokage Danzo who is on his way to the Kage Summit. Agreeing to the new assignment, Madara had Zetsu divide himself and lead Taka to the Summit.

Madara tells the other side of Zetsu that Pain's defeat was a wretch to his plans, and that Outer Path: Samsara of Heavenly Life Technique was supposed to be used on him, and that if Sasuke can't be controlled properly the he is of no use to him. He announced it was time for him to step out of the shadows and commence with his.

The Kage Summit
Gaara the Kazekage of Sunagakure, Onoki the Tsuchikage of Iwagakure and the Current Mizukage of Kirigakure depart from their villages with two guards each as requested by the Raikage to the location of the Summit. Danzo orders ROOT members Dajimu and Terai to continue watching Anko and find Kabuto before she does so she does not discover any experimental data Orochimaru had about his right arm and eye, and orders members Fu and Torune to act as his body guards for the Summit. On the way to the meeting, Danzo is attacked by two assailants and Danzo removes the bandages over his eye to reveal a bloodshot Sharingan.