Pain's Assault (Arc)

The Invasion of Pain arc is from Part II spanning from chapters 419-449. The arc details the attack on Konohagakure by Akatsuki Leader, Pain and his partner Konan.

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.