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Pain's true name is Nagato, and he originates from the Village Hidden in Rain. As a boy, he possessed a kekkei genkai called the Rinnegan Eye, which is a form of Doujutsu that allows the possessor to perform any ninja technique. When he was just a genin, Jiraiya came to his village to help the them prepare for an upcoming war. Jiraiya took a liking to Nagato and his two teammates, Konan and Yahkio, so he helped them train. Jiraiya had also seen that Nagato had the special Rinnegan Eye ability, and helped him develop it as much as he could.

Jiraiya had been under the impression that Nagato was the child destined to change the world, but when Jiraiya left the village, Yahiko was killed, and Nagato came to desire bringing peace by educating people in the suffering that results from war. And thus, he adopted the name "Pain". He then proceeded to gather a few other Rain ninja, including teammate Konan, and started a war with a man named Sanshuoo no Hanzou.

After killing the village leader, Hanzou, and all of Hanzou's friends, family, and associates, Pain became the new leader of the village. To further the image of being god-like, Pain used the jutsu he created to animate six corpses, Yahiko's among them, to serve as his acting vessels, the "Six Paths of Path". Each Path was a master of a form of Jutsu used by Ninja, allowing a decripitized Pain to hide in the shadows and manipulate his puppet bodies.

After a while, Pain and Konan go to Madara Uchiha, the current leader and founder of the Akatsuki Organization. They become members of the Akatsuki, and eventually Pain becomes the leaderhead of the organization.

Shortly after receiving orders from Madara to go after Naruto, Pain encounters his old mentor, Jiraiya, though he does so in the form of his old teammates body, Yahiko. Needless to say, Jiraiya is shocked when he faces Yahiko. Unfortunately, Jiraiya has to take on all six of Pain's bodies, and it is too much for him. With his dying breath from fighting all six powerful opponents at the same time, Jiraiya sent what he learned and Animal Pain's immobilized body to Tsunade to study.

Once animating a new corpse, Pain makes his way to Konoha to start a war with the Leaf Ninja. He kills many before Naruto arrives. Then, after Naruto manages to take out four of the six bodies, Pain attempts to make Naruto understand his ideology by critically injuring Hinata. Nagato nearly succeeded in having Naruto be consumed by the Nine-Tailed Fox and know his pain, but the scheme fails with the death of the last Path (Deva).

In the episodes and the manga it's said that he uses the rain to sense his opponent's chakra or presence.

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