|This is the article on the actual invasion. If you are looking for the article on the story arc, head to Invasion of Pain Arc.|
Pain had been instructed by his benefactor, Tobi, 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. 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 and Hanabi were away when the attack began.
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.
Pain and konan arrived and after eliminating the scouts, began their assault. Fooling the detection teams into thinking there was only one intruder, the six pains scatter, the animal, and Asura path's being the diversions while the rest interrogated and killed for information on Naruto's whereabouts. With their awesome powers, they trashed the leaf, embarrassing their so-called "shinobi", Even Kakashi Hatake, so-called "Master of a thousand techniques", was barely able to make an impression. During these events, they Suddenly changed their strategy, this throwing off the leaf who thought they actually compete with the likes of a badass like Pain. When the human path discovered Naruto's location, after sucking out Shizune's soul, Pain tells the rest to evacuate as he personally reduces the leaf to a smoking heap with a gaping crater in the center. With the ownage complete, Pain prepares to head out and find Naruto, only to be confronted by Naruto after he is teleported back to the Leaf village. A huge battle ensues, highlighted by Hinata's apparent death, Naruto going 9-tails,( sort of), and Pain using his God-like Chibaku Tensei( Planetary devastation technique.) Capping off this amazing battle is Naruto's father, who else but Minato Namikaze, visiting him and inspiring him to fight on without using the 9-tails power. Naruto then proceeds to beat Pain, and travels to his real location, there he talks with a angry Nagato. Naruto convinces him of his Plan, and revives all the villagers he killed. he puts all his trust in Naruto before dying with a smile. Naruto returns to the village, where everyone is waiting to welcome him back. they praise him as a hero, and celebrate him.
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 centre. 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.
While the Deva Path's abilities were recovering from its massive attack, Naruto used his new senjutsu techniques to defeat the other five bodies. Before he could begin fighting the Deva Path, its powers returned. He got rid of Naruto's toad allies and captured him, rendering him immobile with its Chakra Disruption Blades. Defying Naruto's orders, Hinata Hyūga came to his aid, and was struck down and appeared to have been killed, all after revealing her feelings for Naruto. Naruto, in a fit of rage, erupted into his six-tailed transformation.
With the transformation, Naruto gave in to the Nine-Tails' animal instincts in return for power and freed himself from the Deva Path's Chakra Disruption Blades. After charging a Tailed Beast Ball, Pain diverted Naruto's attack, causing another massive explosion to shake Konoha. Needing more chakra to face Naruto's new form, the Deva Path moved to a location closer to Konan and Nagato, Pain's true body. Naruto pursued him, finally giving the village a chance to regroup and tend to the wounded. After getting close enough to Nagato, the Deva Path performed Chibaku Tensei, nearly capturing Naruto in a large, floating sphere of earth. This pushed him into the eight-tailed transformation eventually breaking out of the trap.
After delving into his mind and having the Nine-Tails resealed, Naruto exited the transformation and prepared to face the Deva Path again. 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 sceptical Nagato berated Naruto for trying to stop his plans for peace, despite not even having an alternative plan. Upon hearing Nagato's story and realising how hatred gave birth to Pain, Naruto decided to have faith in their master's teachings and not kill Nagato. Nagato, believing that Naruto would be able to find peace, revived all the people killed during the invasion, sacrificing his own life to do so.
With the villagers revived by Nagato's technique, 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 neighbouring countries reacted to this attack is unknown. After exerting all her chakra to defend the village, Tsunade was left in a comatose state. Naruto, on the other hand, was finally acknowledged as a hero overwhelmingly by the previously hostile villagers. This helped Naruto learn of some of his lineage, along with the experience of loss Sasuke stated he knew nothing of, and would spur Naruto on to find peace.
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 was 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 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.