Over the years, news of the three's exploits would reach Jiraiya which often consisted of the death of someone who opposed them; eventually he received word that they had all died.[7] In truth, Nagato, Konan, and Yahiko began a quest to find peace. They became full-fledged Amegakure ninja and gathered followers who shared their philosophies of an end to war. Hanzō, the leader of Amegakure, viewed the group as a threat to his rule and schemed with Konoha's Root to eliminate them. Claiming to want to discuss peace, Hanzō lured Nagato, Yahiko, and Konan to an ambush. There he forced Nagato to choose between killing Yahiko or Konan. Not wanting to force Nagato to make the choice, Yahiko impaled himself with a kunai that was placed in Nagato's hand. With Yahiko's dying breath, he told Nagato to survive, because he believed in Jiraiya's words that Nagato would become the world's saviour. This would become the second great pain of Nagato's life.
Devastated, Nagato retrieved Konan and Yahiko's body and launched an attack against Hanzō's men. With the Summoning: Demonic Statue of the Outer Path he was able to kill all but Hanzō. However, the technique left Nagato emaciated, with numerous chakra rods embedded in his back. He severed his loyalties with Amegakure by scratching through the symbol of his Amegakure forehead protector, resolving to teach the village and the world his pain. Yahiko's body would later be incorporated into the Six Paths of Pain as the Deva Path.
Upon adopting the alias "Pain", Nagato led the rebelling forces in the Amegakure civil war, and took control of the village by assassinating Hanzō while using his Six Paths of Pain. He then solidified his leadership by systematically killing anyone who had ties to the former leader. At some point he assisted Madara Uchiha in the creation of Akatsuki, using Amegakure as his base of operations.[8]