Pein possesses the Rinnegan, the same eye technique that the first ninja and inventor of the ninja world possessed, whom was called Rikudou. The Rinnegan is said to be the most illustrious of the three eye techniques, said to be a tool of god that can either bring salvation or destruction. He is a man that has grown through the pain and experiences of life. Pein stays emotionless through most of his appearances. He only speaks to Konan when not involved in giving orders or sealing tailed beasts. Pein's talents allow him to peg himself as a deity given right to lay judgment upon others. He believes only by invoking true suffering can people learn what to treasure. This is the only way he feels the world will be able to know true peace.
Origin
Usurping Hanzo
Pein lead one side of a civil war in the Rain village and killed Hanzo, thus becoming the new leader of the Rain village. But he didn't stop with Hanzo, he killed Hanzo's family, friends, and associates. Nobody in the village knows whether or not Pein really exists, everything known about him is from rumors. They've never seen him fight and they don't even know how he killed Hanzo. The people however respect Pein and revere him as a god, if only out of respect. They only know that he his base is the highest building in the village where he watches over all of them.
During the sealing of the Three-Tailed Demon, Hidan became frustrated and wanted to know what Pein's plan is. Pein explained that Akatsuki is going to be a ninja monopoly. Pt. 1 of the plan is that they are gathering money to help establish a an independent Shinobi village, paying no allegiance to any country. Pt. 2 is to offer their services for a mere pittance of what other villages would charge, even using the Bijuu they capture to stir conflict. That comes to pt. 3. the other ninja villages will go broke and the countries that rely on them for security and revenue will collapse, that is where Akatsuki will step in and effectively rule the world.
Pein and Konan
After Deidara died, Konan and Pein await on the arrival of a shadowed figure. This shadowed figure tells them of Sasuke's potential. This person then tells Pein to order the remaining members to capture their Bijuus and tells Pein to capture Naruto, but warns him of Naruto's power. Konan interjects, reminding their guest that Pein has never been defeated, which returns a laugh from the mysterious person. As the person begins to leave, he reminds them how by working together that both of their goals will be achieved... and is revealed to be none other than Tobi. After Tobi departs, Konan comments "the sky is crying. Pein, you..."
From his base, he realized due to an obstruction in his rain's fall that someone had entered his village, someone dangerous, though he does not realize it is Jiraiya. He stops the rain for Konan to send out her origami spies to find the intruder. After she left, he went into a room with 6 tables and 5 bodies laying on those tables. He laid down on the empty table, closed his eyes, then he left to find the intruder in another body, his Beast Realm body.
He found Konan being questioned by Jiraiya and freed her with a summon, a giant lobster. However Jiraiya destroyed his summon and captured Pein and started questioning him. Confident in his victory, he decided to tell Jiraiya his plan. He was going to use the bijuu to create a new technique which would destroy entire countries, he believes the pain this technique causes will stop people from fighting ever again. But when Jiraiya dealt the death blow, it was revealed that Pein used a substitution technique to escape, he then appeared riding a chameleon-like chimera. Pein went inside the chameleon's mouth and they became invisible, and Jiraiya summoned a giant toad to defend him while he prepared to use a technique. Pein then summoned a giant multi-headed dog that spit into many different dogs, a giant bird, and a giant yak, but they were all defeated.
Jiraiya unsummoned the giant toad before it got too hurt and activated Hermit Mode, and the two new toad summons on his shoulders destroyed Pein's chameleon-like chimera, Pein summoned two of his other 5 bodies, the Hungry Ghost Realm and Human Realm bodies. Human attacked first but was struck aside and blinded, impressing Pein. Hungry Ghost then blocked and absorbed Jiraiya's ninjutsu. Jiraiya used another ninjutsu directed at Hungry Ghost, but once again he blocked and absorbed the technique. When Human attempted to attack Jiraiya from behind, one of Jiraiya's summons created a smokescreen as Jiraiya countered and attacked Hell, but thanks to one of the Rinnegan's uses, was able to block the "unseen" attack by being able to see what the other bodies see, but Jiraiya didn't realize this fact right away and attacked the distracted Beast from behind, but Beast summoned a stone Panda to block Jiraiya's attack. Pein's bodies regrouped after Jiraiya's attacks and prepared to attack, but Jiraiya disappeared and Pein realized that Jiraiya was hiding in the surrounding pipes and ran along-side them, listening. He heard Jiraiya's summons croaking and chased after. Pein found Jiraiya but was surprised by Jiraiya's Shadow Clone, Hungry Ghost attempted to protect the others from the Shadow Clone's fire technique but was engulfed and unable to see, then Jiraiya trapped Human, leaving only Beast and Jiraiya.