Pain's Assault

The Invasion of Pain was the attack on Konohagakure by the Akatsuki leader, Pain, in search of Naruto Uzumaki, the host of the Nine-Tailed Demon Fox.

Background
Pain had been instructed by his benefactor, Madara Uchiha, to capture Naruto. When Jiraiya infiltrated his village, Amegakure, Pain was forced to deal with him before he could go after Naruto. Although he was able to kill Jiraiya, Pain had permanently lost one of his six bodies and had to find a replacement before he could move on to Konoha. During the battle with Jiraiya, Fukasaku managed to escape the battle with knowledge about Pain.

With the information gathered from Fukasaku, the body Jiraiya had defeated, a prisoner he had captured, and a coded message he had made before his death etched on the back of Fukasaku, Konoha had ample sources of information concerning Pain. While some of Konoha's forces dedicated their time to deciphering what Jiraiya had left to them, the rest of the villagers prepared for Pain's arrival. Shikamaru worked with Shiho and the Konoha Cryptanalysis Squad in deciphering Jiraiya's dying message about Pain. Shizune was in charge with doing the autopsy on the recovered body while the Konoha Torture and Interrogation Force was tasked to collecting information from the captured Shinobi.

The defensive measures that had been erected since the last time the village was attacked were presumably built upon. Many of the Konoha ninja were kept home. However, Konoha still took part in its ninja mission business. Team Guy, Hiashi Hyūga and Hanabi Hyūga were away when the attack begins.

Naruto, knowing that Pain would be coming for him, decided to make use of the time Jiraiya had bought for him. He went to Mount Myōboku, the home of the toads, to learn senjutsu for his inevitable encounter with Pain. Kōsuke was left in Konoha to send word to Naruto when Pain eventually arrived.

Attack
Pain and his partner Konan arrived on the outskirts of Konoha and eliminated all of the village's scouts. As the village was surrounded by a detection barrier, Pain's Animal Path was sent in to the village alone to fool the Barrier Team, leading Konoha to believe there was only one invader. After infiltrating the village, the Animal Path summoned Konan and Pain's other five bodies to its location, where they dispersed.

The Animal Path, the Asura Path, and the Preta Path acted as diversions. The Animal Path summoned a variety of creatures to draw Konoha's attention. The Asura Path used its many weapons to wreak havoc and destroy most of the village. The Preta Path engaged whatever forces it came upon. Konan, the Deva Path, the Human Path, and the Naraka Path dedicated their efforts to finding Naruto. The Human Path read the villagers' minds. The Naraka Path asked those he encountered what they knew and then used its abilities to see who was lying. Konan and the Deva Path used the threat of death to find out what they wanted.

In the initial phase of the attack, Konoha mobilized its forces, expecting only one intruder. Once it became apparent that there was more than one attacker, the village switched tactics, focusing in on the diversionary Paths. The ordinary citizens and those that had been injured in the initial wave fled to the Konoha hospital. Sakura Haruno provided defence for the hospital and healed what injuries she could. Tsunade, the Fifth Hokage, instructed Kōsuke to call back Naruto. Danzō, having other plans, killed Kōsuke to keep Naruto from returning. From the roof of the Hokage Residence, Tsunade summoned Katsuyu. Tsunade then had Katsuyu divide, seek out, and adhere to every villager so that she could tend to the entire village remotely.

Kakashi Hatake, recognizing Pain's plan, engaged the Deva Path in battle. The Asura Path came to the Deva Path's defence. Although Kakashi was able to defeat the Asura Path, he could not defeat the Deva Path as well. He had Chōji Akimichi, who he had fought beside, take knowledge of the Deva Path's abilities to Tsunade while he bought time. While Chōji informed Tsunade of what they had learned, Kakashi died from exhaustion from using the Mangekyō Sharingan to protect Chōji from Asura Path's missile.

Across the village, Konan and Pain's remaining bodies began attracting the attention of Konoha's defenders. The Animal and Preta Paths then switched objectives. The Animal Path assaulted the location where Jiraiya's prisoner was being held and tried to eliminate everyone at the location. The Preta Path found and disposed of the body (and its chakra receivers) that Jiraiya had captured. The Deva Path located and spoke with Tsunade, but became irritated by her words. When the Human Path captured Shizune, Pain was able to discover where Naruto was.

The Deva Path had Konan and the remaining Paths evacuate while it used a large-scale Shinra Tensei to destroy the village and teach Tsunade "true pain." In a brief moment between when the destruction began and when it was completed, Tsunade had the remaining Katsuyu copies shielded the hospital. Tsunade also dedicated what was left of her chakra to keeping the villagers safe. In the wake of the destruction, all that remained of Konoha was a large crater, the Hokage Monument, and huge amounts of debris, ruins, and half-destroyed infrastructures.

Counterattack
Shima, having been near Konoha, noticed that something was wrong. In unison with the village's destruction, she summoned Naruto, Gamabunta, Gamaken, Gamahiro, Gamakichi, and Fukasaku to the village's center. When the dust cleared, Pain and his six bodies (the Asura Path having been restored by the Naraka Path), gathered to face Naruto. Before they fought, however, a weakened Tsunade angrily vowed to make Pain pay for destroying Konoha. When Asura Path attacked Tsunade, Naruto quickly defeated him in one blow. After discovering that Kakashi had been killed, Naruto instructed the rest of the villagers not to interfere with the fight, knowing that it would be hard to fight and protect them simultaneously.

Pain's Animal Path summoned a number of animals to attack Naruto, who used the increased strength granted to him by Sage Mode to bat them aside to his toad allies. While they dealt with the summons, Naruto disposed of the Preta Path with Frog Kata before preparing the fruits of his senjutsu training: a perfected Rasenshuriken. He hurled the attack at Pain's remaining bodies, and it expanded when it neared them, disintegrating the Human Path. Running low on chakra because of the attack, Naruto had Gamabunta trap the Animal Path in his mouth, where Naruto was able to defeat it with his Rasenrengan without interference from the other bodies.

Having run out of natural energy and thus having exited Sage Mode, Naruto had Fukasaku summon one of his shadow clones from Mount Myōboku. As a workaround for his inability to have a constant supply of natural energy, he had had some of his shadow clones gather it for him. Revitalized, Naruto attacked with another Rasenshuriken, only for the Preta Path to appear and absorb the attack. Realizing that the Naraka Path must have restored it, Naruto focused his efforts on getting rid of it. He distracted the Deva Path with a smokescreen, and landed another Rasenrengan on the Naraka Path, defeating it.

Though he had defeated four of Pain's six bodies, Naruto was captured through a combination of efforts from the Deva and Preta Paths. The Preta Path absorbed his chakra to make sure he was no longer a threat but, being unable to handle natural energy, the Preta Path turned into a frog statue, allowing Naruto to free himself. The Deva Path captured Naruto again using his Chakra Disruption Blades, and killed Fukasaku when he tried to come to help. While immobilizing Naruto, the Deva Path told Naruto of his plans for world peace. When Naruto disagreed with his views, Jiraiya's death being a by-product of that peace, the Deva Path asked Naruto for a better solution. Before he could answer, Hinata came to intervene. Naruto demanded her to stay away from the fight, but Hinata remained where she stood and confessed her love to Naruto (greatly shocking him), and fought against the Deva Path in a futile effort to save him. When she was apparently killed, an enraged Naruto exploded into his six-tailed transformation.

His necklace reacted in an effort to quell the transformation, but the Nine-Tails quickly destroyed it and attacked Pain. Unable to deal with this new threat, the Deva Path retreated to a location closer to Nagato and Konana, where it could use Chibaku Tensei, drawing in and containing Naruto. Within his subconscious, Naruto thought of Pain's plans for peace, and pleaded for someone to help him with a response. Through his suffering, the Nine-Tails tempted Naruto to entrust his heart to it so that it could destroy everything that was causing Naruto pain, thus distorting the seal to the point where the eight-tailed form was released, breaking free of the Chibaku Tensei. This pushed him into the eight-tailed transformation eventually breaking out of the trap. Before he could completely release the Nine-Tails, however, his father, Minato Namikaze, appeared in Naruto's subconscious to stop him.

Minato revealed that he had designed the seal of the Nine-Tails to allow an imprint of himself to appear if ever the seal was about to break, a failsafe meant to protect his son. Picking up on this, Naruto realized that the Fourth Hokage was his father, and was overjoyed to finally know who one of his parents was. His time being short, Minato revealed that he had sealed the Nine-Tails into his own son because he thought Naruto would someday find use for it in finally stopping [Madara Uchiha. They also discussed the concept of peace, and Minato revealed that hatred gave rise to Pain, and that ninja must find a way to end the hatred. While Naruto doubted that he could do it, Minato replied that he believed Naruto would be able to find the answer, and restored the Nine-Tails' seal before disappearing.

Outside, Naruto emerged from the Chibaku Tensei, with the Nine-Tails' influence gone and Sage Mode having returned. Knowing that its abilities needed 5 seconds to recharge, Naruto used an elaborate array of backup plans to eventually defeat the final path with a Rasengan to the chest. After winning the battle, Naruto went to meet with Nagato.

A skeptical Nagato berated Naruto for trying to stop his plans for peace, despite not even having an alternative plan. Naruto admitted that he hated Nagato, but restrained himself long enough to ask how Nagato, a fellow student of Jiraiya, turned out this way. After hearing Nagato's past and his reasons for desiring war, Naruto agreed on some points, but rejected the overall conclusion on the grounds that it differed from Jiraiya's ideals. To break the cycle of hatred, Naruto told Nagato and Konan that, despite hating them, he would not kill them, Naruto deciding to have faith in their teacher's teachings and not kill Nagato. Nagato, believing Naruto would be able to find peace, revived all the people killed during the invasion, sacrificing his own life to do so.

Aftermath
With the villagers revived by Nagato's jutsu, Konan, having lost the only person left she cared about, decided to leave Akatsuki. She also promised that Amegakure would help Naruto achieve his and Nagato's vision of peace. Though their ninja force was revived, the village itself was left in ruin. How the neighboring countries reacted to this attack is unknown. After exerting all her chakra to defend the village, Tsunade was left in a comatose state. The Fire Daimyō and the rest of the village's governing body assembled, and Danzō was appointed by the Fire Daimyō as the acting Sixth Hokage until a vote of confidence can be held. His first act as the acting leader is to have Sasuke Uchiha classified as a missing-nin and marked for assassination. At this point an envoy from Kumogakure arrived with a request from the A|Raikage for all information regarding Sasuke Uchiha. At virtually the same time, the courier bird arrived from Kumogakure with the invitation to the Summit of the Five Kage.