Arc 3Pain Takes Amegakure
Nagato and Konan defeated Hanzo, took control of Amegakure, and built a hidden laboratory to develop Nagato’s second body, Kaede. As Nagato strengthened his organization and sent Pain A toward Iwagakure, Jiraiya learned that the attacker at Konoha had the Rinnegan and set out to investigate Amegakure.
- Nagato fled Obito’s attack with Konan and Orochimaru, then resolved to take Amegakure from Hanzo while Konan traveled separately with Pain Rin.
- Pain Rin and Konan encountered Kakuzu, and Nagato’s Paths defeated him and made him the temporary Naraka Path before Nagato’s forces entered Amegakure.
- Hanzo fought Nagato’s Paths and summoned creatures, but Nagato’s forces overcame him, and Hanzo asked Nagato to lead Amegakure before he died.
- Nagato eliminated Hanzo’s associates, declared Pain a god through Konan, and captured Darui, Samui, and C as candidates for Amegakure’s future Three Ninja.
- Nagato and Orochimaru established a hidden laboratory, grew a second body named Kaede, and tested how Nagato’s consciousness could synchronize with a living body.
- Orochimaru injected Nagato with purified Hashirama Artificial Body Cells, while Konan trained alone and later collapsed from exhaustion after using Black Rods to sustain herself.
- Orochimaru revived Kakuzu with Impure World Reincarnation, and Kakuzu agreed to serve as Amegakure’s financial steward in exchange for forty percent of yearly profits.
- Nagato learned that Jiraiya had returned to Konoha, dealt with Root infiltrators, and used the bounty on their corpses to fund Amegakure while considering a replacement for Pain’s Human Path.
- Pain A and Pain Rin departed for Iwagakure to retrieve Mu, while Minato told Jiraiya that the attacker at Konoha had the Rinnegan matching Nagato’s eyes.
- Jiraiya considered that Nagato’s Rinnegan might have been stolen, received Minato’s intelligence, and headed toward the western border of the Fire Country to investigate Amegakure.