Pain's Assault

The Invasion of Pain was the attack on Konohagakure by the Akatsuki leader, Pain, in search of Naruto Uzumaki, the container 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 lost one of his six bodies and had to find a replacement before he could move on to Konoha. Furthermore, one of Jiraiya's toads had managed to escape with knowledge of him.

With the information gathered from the toad, the body Jiraiya had defeated, a prisoner he had captured, and a coded message he had made before his death, 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. 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 Hyuga and Hanabi Hyuga 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 Myōbokuzan, 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 wreck havoc and destroy 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 defense for the hospital and healed what injuries she could. Tsunade, the Fifth Hokage, instructed Kōsuke to call back Naruto. However, Danzo, 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 defense. Although Kakashi was able to defeat the Asura path, he could not defeat the Deva path as well. He had Choji Akimichi, who he had fought beside, take knowledge of the Deva path's abilities to Tsunade while he bought time. While Choji informed Tsunade of what they had learned, Kakashi was defeated by the Deva path.

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 scaled 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 shield 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 at the time, had earlier noticed 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), faced Naruto. Taking the village's destruction personally, Naruto instructed the rest of the villagers not to interfere with their fight.

With the Deva path momentarily unable to do anything because of its destruction of Konoha, Naruto was able to use his new senjutsu techniques to defeat the other five bodies. Before he could finish off the Deva path, its powers returned. It got rid of Naruto's toad allies. It also captured him, rendering him immobile with its Chakra Disruption Blades. Defying Naruto's orders, Hinata Hyuga comes to his aid. Hinata was struck down and appeared to have been killed, after revealing her feelings for Naruto. Naruto, in anger, advances to his six-tailed transformation.

With the transformation, Naruto gives in to the Nine-Tails' animal instincts in return for power. He is able to free himself from the Chakra Disruption Blades. He tries to attack the Deva path with a Six-Tailed Fox Menacing Ball. Pain diverts the attack at the last minute. It goes astray, punching a hole through the rubble of the village. Recognizing the danger of Naruto's new form, the Deva path retreats to a location closer to Konan and Nagato, Pain's base mind. Naruto pursues him, finally giving the village a chance to regroup and tend to the wounded. The Deva path uses Chibaku Tensei and almost captures Naruto. Naruto then goes into eight-tailed transformation to counter him.

After some soul searching, Naruto turns back to normal and fights the Deva path. Using the fact that the path needs five seconds between its attacks to "recharge", Naruto is able to defeat it. After winning the battle, Naruto goes to meet with Nagato. They have a conversation about how best to bring peace to the world. Upon hearing Nagato's story and the chains of hatred, Naruto decided to have faith in their teacher and not kill Nagato. Nagato was so moved that he revived all the people killed during the invasion. However, he had sacrificed his life to do so.

Aftermath
With the villagers alive, Konan, Nagato's partner, decides to leave Akatsuki. She also says that Amegakure will help Naruto achieve his and Nagato's vision of world peace. Though their ninja force was revived, the village itself was left in ruin. How the neighboring countries will react is currently unknown. Since Tsunade was in a comatose state, Danzo was elected by the Fire Daimyo as the acting 6th Hokage. He allows the ANBU to begin the hunt for Sasuke Uchiha.