nagato died and his partner stole his rinnengan and took 6 ninjas and made paths with rinnengan and now he is pein the strongest ninja who defeated every battle but almost lost against jiriya sensei the ninjas that were the 6 paths jiriya beat and didn't figure out there power and peins identity and peins the akatsukis leader and works with konan the akatsukis woman and paper angel
p.s nagato died and he was always good!
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Nagato was considered a bad guy at first, but changed to a good guy before he died.
Nagato in naruto is pein.Nagato became pein in the 2nd great ninja war.Jiraiya took him,yahiko,and konan as his students.Now nagato is the akatsuki member known as pein.Pein is not the lleader of the akatsuki though.
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all of the pains are controlled by Nagato. The pains appearence comes from Yahiko who was another orphan during the second shinobi world war. Yahiko nagato and konan were all very good friends. They all wanted the war to stop and desired peace.Yahiko died and told nagato to continue their search for peace. When yahiko died nagato was enraged and used a jutsu. Then he continued their "search" for peace. Hope that answers it but i was still a little confused. Sorry about my bad grammer!
After Konan died Madara (Tobi) found Nagato's body and he transplanted Nagato's rinnegan into his left eye.