Pain's Assault (Arc)

The Invasion of Pain arc is from Part II, spanning from chapters 419-449. The arc detailed 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, Human, Animal, and Naraka paths, 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 often 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 immobilize Naruto, Pain then pinned him to the ground with his Chakra Disruption Blades in order to take him away. Before departing, Naruto asked Pain why he had done everything, to which Pain replied that the world could never have the peace Jiraiya fought for because the world was too full of hatred, and, therefore, the only way to create world peace was 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 would prevent more fighting.

Shikamaru Nara, having survived the destruction of Konoha, met with the Yamanaka group carrying Shizune's body. When they were 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 was describing his quest for world peace, his true body, Nagato, emaciated and with several chakra blades sticking out of his back, was shown in his and Konan's hiding place, a makeshift tree on a high mountain close to the village. Hinata Hyuga came to his rescue after confessing her love for Naruto, but was quickly struck down and fatally wounded. Believing her dead, Naruto lost control of his anger, and slipped into his six-tailed transformation. With the Nine-Tails in control of Naruto's body, it fought and overwhelmed Pain, causing him to retreat from the village in order to get close enough to Nagato to use Chibaku Tensei. With the Nine-Tails controlling Naruto, and Pain out of the village, Sakura Haruno ordered all who could 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, sensed that Naruto had released six tails of the Nine-Tails, and headed back to find and stop Naruto.

While still being pursued by the Nine-Tails, Pain, through the great strain of Nagato, used the Chibaku Tensei to create a giant miniature moon in an attempt to capture the Nine-Tails. During this time, Naruto, locked in his own subconscious and lost in despair, called out for help to a response of Pain's visions of peace. In the end, while the apparently evil Pain had a plan to deal with the hatred in the world, Naruto did not. Taking advantage of his pain, the Nine-Tails convinced Naruto to destroy everything in the world by releasing the seal. This caused 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 Nine-Tails into him because he too felt that the Nine-Tails was forced to come to Konoha, and believed a masked being within Akatsuki was behind the attack. After easing Naruto's fears that he couldn't change the world, Minato repaired the seal and sent Naruto back to finish his battle with Pain.

With the Nine-Tails' 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 had made him the way he was. Nagato, still wanting to know Naruto's reply to his question, answered with two stories. The first was how his parents were killed during the Second Great Shinobi World War, which led 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 had revealed to the small makeshift family that he wanted to rule the world, to stop the world's wars. After their dog, Tiny, was killed by an exploding tag as collateral damage from the Sannin's battle with Salamander Hanzō, Yahiko declared he wouldn't just rule the world, but would become a god, a dream that sparked the same desire in 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, when a "messiah", the Sage of the Six Paths, appeared, and spread his religion across the world, which came to be the ninja techniques that the shinobi used 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, led by Yahiko, to abolish wars and bring peace to 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 an 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 in order to use the latter's chakra. The statue then released a soul removing dragon which 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 told Naruto that he had become the leader of their gang, and had carried on Yahiko's agenda to bring peace to the world.

After hearing Nagato's story, Naruto reflected on everything he had heard. Naruto agreed that some of the things Nagato mentioned were true, but he also said that Jiraiya had believed in him, and that he would believe in what Jiraiya had believed in, and that was why he would not kill Nagato. Nagato questioned this, and Naruto pulled out the book that Jiraiya had written. He began reading from it, and told Nagato the main character's name was Naruto. Naruto then said that he would become Hokage, and he promised peace for Amegakure as well. Nagato then stated that Naruto was like him when he was younger. He said that he would believe in Naruto, and prepared to use a jutsu.

Upon using the jutsu, Nagato used 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 was shown telling Gamabunta that everyone had been revived, and that he found 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 decided to leave, and took both Nagato and Yahiko's bodies, telling Naruto that she would believe in him. She then used her paper jutsu to create a bouquet of flowers, and gave them to Naruto.