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, and many of the Konoha ninja were kept home. Konoha still took part in its ninja mission business, Team Guy, Hisashi Hyuga and Hanabi Hyuga being 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 Myobokuzan, the home of the toads, to learn senjutsu for his inevitable encounter with Pain. Kosuke 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, and 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 reading the villagers' minds, the Naraka path asking what those he encountered knew and then using its abilities to see who was lying, and Konan and the Deva path using 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, where Sakura Haruno provided defense and healed what injuries she could. Tsunade, the Fifth Hokage, instructed Kosuke to call back Naruto, but Danzo, having other plans, killed Kosuke to keep Naruto from returning. From the roof of the Hokage Residence Tsunade summoned Katsuyu, who she then had 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 and, although Kakashi was able to defeat it, 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. Kakashi was quickly defeated, but Choji was able to inform Tsunade of what they had learned.
Across the village Konan and Pain's remaining bodies began attracting the attention of Konoha's defenders. Found out, the Animal and Preta paths switched objectives; the Animal path assaulted the location where Jiraiya's prisoner was being held and tried to eliminate all present, and 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 immediate objective complete, 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 the brief moment in time between when the destruction began and when it was completed, Tsunade had the remaining Katsuyu copies shield the hospital and 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 infrastructure.
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 and captured him, rendering him immobile with its Chakra Disruption Blades. Defying Naruto's orders, Hinata Hyuga comes to his aid. When she is struck down and appears to be killed, Naruto, in anger, advances to a six-tailed demon fox form.
With the transformation, Naruto gives in to the demon fox's animalistic instincts in return for power. He is able to free himself and tries to attack the Deva path with a Six-Tailed Fox Menacing Ball. Pain diverts the attack at the last minute and 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. There, Deva path uses Chibaku Tensei and almost captures Naruto as he goes into eight-tailed demon fox form to counter him.
After some soul searching, Naruto turns back to normal and fights the Deva path. Using the the fact that the path needs five seconds between its attacks to "recharge", Naruto is able to defeat it. The battle won, Naruto goes to meet with Nagato and has a conversation about how best to bring peace to the world.
Conversation Between Jiraiya's Students
he battle won, Naruto seeks out Nagato, Pain's base mind, to finally answer his earlier question about peace. Naruto admits to his raw anger and hatred towards Nagato, but he holds his ground and asks Nagato how he turned out this way after being Jiraiya's student. After hearing Nagato's past, Naruto agrees that on some points, Nagato is right, but he shocks both Nagato and Konan as he declares that despite hating them, he will not kill them, simply for his desire to "break the cycle of hatred" and his answer is to believe Jiraiya's idea in peace.
Amazed by Naruto's determination to his answer, Nagato said that he would believe in Naruto and revives all the people Nagato killed in Konoha at the cost of Nagato's life. With this, Naruto helps Konan retrieve Nagato and Yahiko's body for burial in Amegakure. He confirms that she has quit Akatsuki and taken leadership of Amegakure, she leaves Naruto a bouqet of paper flowers for him, symbolizing their new found alliance.
Is this Story Arc Over?
Pain Dead...
Konan will now lead the Amegakure...
Sasuke now departs with his team. Going to Konoha....
Whats next?
Interesting Manga To read. +
Nice Anime to watch(which is now on the 3 Tails Filler Arc.)
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