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The Six Paths of Pain and Konan arrive on the outskirts of Konoha and eliminate all the border guards. Pain explains the plan of attack: the Asura, Animal, and Preta Paths will destroy the village's infrastructure and draw the attention of its ninja while Konan and the Deva, Human, and Naraka Paths try to find information on Naruto's location. The Animal Path infiltrates the village by itself so that Konoha's sensors will think there's only one intruder, and once inside it summons Konan and the others. They scatter immediately afterwards and begin fulfilling their assigned roles. Early in the Deva Path's search it is found by Kakashi Hatake, who has guessed the misdirection Pain is employing. Knowing by reputation that Kakashi poses a threat to Akatsuki's plans, the Asura Path arrives to help the Deva Path fight him. The two nearly defeat Kakashi, but Konoha reinforcements arrive in time. Kakashi has already discovered the recharge time the Deva Path needs between attacks and coordinates Konoha's forces to create a window for him to strike. The Asura Path uses itself as a shield to take the attack, creating an opportunity for the Deva Path to level everything and everyone in the area. The Deva Path leaves, victorious. After it's gone, a badly-injured Kakashi sends Chōji Akimichi to the Fifth Hokage to tell her what they've learned about the Deva Path. The still-functioning Asura Path attempts to stop Chōji, but Kakashi intercepts it with Kamui in time, dying from exhaustion in the process. Across the village, the remaining Paths continue their tasks: the Preta Path locates the Animal Path that Jiraiya captured and collects its black receivers; the Deva Path locates the Hokage and encourages her to surrender Naruto; the Animal Path assaults the building where a prisoner Jiraiya captured is being interrogated, killing him in the process; the Human Path discovers Shizune and, from reading her mind, finally learns that Naruto is at Mount Myōboku. Though their mission is complete, Pain is frustrated by the Hokage's refusal to cooperate. Combined with the numerous examples that Konoha's ninja are starting to understand how the Six Paths of Pain work, Pain decides to destroy the village and show it true pain. He has the Animal Path summon Konan and all but the Deva Path to a safe distance while the Deva Path performs a large-scale Shinra Tensei. As the smoke clears, the Deva Path finds Naruto has arrived in the village with several toad allies. After the Naraka Path restores the Asura Path, the other Paths join the Deva Path; Konan withdraws to attend to Nagato. When the Hokage angrily confronts Pain for destroying the village, the Asura Path moves to kill her, but is destroyed by Naruto before it can land a blow. The remaining Paths take formation around the Deva Path during its prolonged recharge. The Animal Path sends its summons to attack Naruto, but the toads confront them instead. Using Sage Mode, Naruto quickly neutralises the Preta Path, the Human Path is destroyed getting the Animal Path out of the way of Naruto's Rasenshuriken, and the Animal Path is shortly afterwards trapped within Gamabunta's mouth and defeated with Spiralling Serial Spheres. Naruto begins focusing on the Deva Path. He nearly succeeds in hitting it with another Rasenshuriken, but a restored Preta Path absorbs it. Seeing what the Naraka Path can do, Naruto prioritises it, distracting the Deva and Preta Paths while he hits it with another Spiralling Serial Spheres. Although the Naraka Path is gone, the Deva Path's powers are restored. It expels the larger toads from the village and helps the Preta Path capture Naruto. As the Preta Path absorbs his senjutsu chakra to immobilise him, it finds itself unable to balance the natural energy and turns to stone. Shima and Fukasaku, meanwhile, prepare to cast a genjutsu like they did before. The Deva Path kills Fukasaku and, in the same motion, pins Naruto down with black receivers. With Naruto no longer able to offer resistance, Pain lectures him on the cycle of hatred the world suffers under and the endless conflict that produces. His plans to gather the tailed beasts will be used to cause overwhelming destruction and achieve peace through fear. Because peace is what Jiraiya, who both of them trained under, always wanted, Pain asks if Naruto has a better solution, but Naruto does not respond. As they talk, Pain is attacked by Hinata Hyūga, who makes a desperate attempt to save Naruto. The Deva Path deals with her easily and apparently kills her. Her seeming death enrages Naruto, causing him to enter a version 2 state. Unprepared to fight Naruto in this state, the Deva Path leads Naruto closer to Nagato's location so that it can use Chibaku Tensei. Naruto enters a nearly full Tailed Beast Mode and escapes its confines, forcing Pain to let the Chibaku Tensei dissolve. Having regained his senses, Naruto attacks the Deva Path. He takes one of its black receivers and briefly interfaces with it in order to trace Nagato's location. As his attack continues, he has numerous disguised shadow clones emerge from the rubble of Chibaku Tensei and attack during the Deva Path's short cooldown, but they don't make it in time and it repels them. With so many clones, however, the Narutos are able to resist the Shinra Tensei, enabling Naruto to strike with a Rasengan. Now that all of his Six Paths are defeated, Nagato permits Naruto to come meet with him. He shoots Naruto with a black receiver as soon as he arrives and tries to control his body, but Naruto successfully resists him. Naruto has been thinking about the question he was asked earlier, about how he would accomplish peace. He thinks he has an answer finally, but first wants to hear more about Nagato, especially since they both trained under Jiraiya yet turned out very differently. Curious, Nagato indulges him and tells him about the tragedies he experienced in his life and how they drove him to seek peace through pain. Naruto understands Nagato's logic and even sees some merit to his conclusion, but rejects it. His method to achieve peace is to no longer continue the cycle of revenge that fuels the shinobi world. Although he is angry with Nagato for killing Jiraiya and destroying Konoha, Naruto will not harm him, as that would only cause others to seek revenge against him and repeat the cycle. Nagato is amazed by Naruto's answer, and is reminded of not only Jiraiya but himself when he was younger. He does not know if Naruto's solution can succeed, but Nagato decides that he will place his faith in it. As a sign of this faith, Nagato uses Samsara of Heavenly Life Technique over Konan's protests to revive everyone that died during his attack. As his life fades from performing the technique, Nagato cautions Naruto over the challenges he will face on the path he has chosen, but wishes him all possible luck. Nagato dies with a smile on his face, wondering if perhaps all the circumstances that led him to this end were the work of a real god.

When the Fourth Shinobi World War begins, Nagato is mobilised with the rest of Kabuto's collection of reincarnated ninja. Still unable to move even in his reincarnated state, Nagato is carried by Itachi Uchiha. They discuss Akatsuki and how little they, particularly Nagato, actually knew about the organisation; both were only pawns kept by Tobi because of their dōjutsu, and now they've been revived so Kabuto can use them for the same reason. Nagato is at least able to sense where Kabuto is controlling them from, which he communicates to Itachi. Nagato and Itachi are found by Naruto and Killer B. Nagato is glad to see Naruto has finally gained control of the Nine-Tails, but is not actually surprised since they both trained under Jiraiya. Kabuto forces Nagato and Itachi to attack them, with Nagato summoning various animals to help him move around. Because their personalities are intact, Nagato gives Naruto and B advice about how to counter his summons and jutsu and warns them about Itachi's own. Itachi is able to implement a fail-safe he left on Naruto before his death, which frees him from Kabuto's control. Fearful that Nagato may also break his control, Kabuto suppresses his personality and sends him into battle against the trio. Itachi joins forces with Naruto and B against Nagato. Nagato hides within his chameleon so he can move around undetected and attacks B with Shinra Tensei. B immediately counters with a version 2 Lariat, resulting in Nagato absorbing B's version 2 chakra. The Eight-Tails' chakra he absorbs has a rejuvenating effect on him, restoring his mobility. He begins removing Naruto's soul, prepares to kill B, and readies the King of Hell to restore them to life when Kabuto is ready for them. Itachi interrupts him with Susanoo, releasing Naruto and B. Needing to deal with all three at once, Kabuto has Nagato use Chibaku Tensei. Itachi, Naruto, and B simultaneously use their strongest long-range attacks to destroy the growing planetoid. As Kabuto's attentions are distracted by its destruction, Itachi stabs him with Susanoo's Sword of Totsuka, which also restores his consciousness to him. Nagato apologises to Naruto for not only this fight after death, but his actions during life, believing his story was unworthy of following Jiraiya's. He expresses his hope that Naruto's story will conclude so spectacularly that nobody will remember the disappointment of his own. He bids farewell as his body is sealed.