Pein's Background

Pein is at first believed to be a boy named Nagato, who, like Konan and Yahikowere orphans from Amegakure, forcing them to fend for themselves.The three eventually encountered the Sannin who at first was less than willing to help them. Orochimaru even suggested to kill them as they were orphans of war and as such would only live their lives full of misery.Jiraiya, however, decided he would care for the three and took them in. One night at dinner, Nagato cried because eating together reminded him of his family, and later that night he ran away with Yahiko.
The two were attacked by a Rock chunnin who injured Yahiko. Seeing this, Nagato activated his Rinnegan, and killed the ninja, a feat that is normally impossible for someone who has never trained as a ninja or never had any military training or martial arts training. Jiraiya decided then and there he would train them in ninjutsu. Nagato was very emotional about killing the shinobi, and asked Jiraiya for help so he can protect Konan and Yahiko, where Jiraiya said he must grow up. After three years, Jiraiya felt they were strong enough to fend for themselves and told the three he would see them again when they grow into adults. Jiraiya believed Nagato to have died with the others under unexplained circumstances, but has told Konan that whenever their names were mentioned outside their village, it was always about someone being killed when they opposed them.
Pein has since led one side of Amegakure to taking over the village and has become a greatly respected leader in that village. When Madara Uchiha founded Akatsuki is unknown but Pein is situated within Amegakure. The members of Pein's faction wear their Amegakure forehead protectors with a scratch through it the way the full members of Akatsuki do.