Nagato

is the recognized leader of Akatsuki and a missing-nin from Amegakure. He is referred to as "leader" by all Akatsuki members except for Konan, who refers to him by his name. Although he directs the actions of the other members and maintains authority over them, Pein takes orders from Tobi, who is actually Madara Uchiha. In addition to acting as Akatsuki's leader, Pein was the leader of of the winning faction in the Land of Rain's latest civil war; When he was a child, himself going by Nagato, Konan, and Yahiko were orphans trained by Jiraiya for three years.

Background
When he was younger, he, Konan, and Yahiko were orphans from Amegakure, forcing them to fend for themselves. The three eventually encountered the Sannin, who at first where 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 day for dinner, Nagato cried because eating dinner together reminding him of his family and later that night he ran away with Yahiko.

The two where attacked by a Rock shinobi, who injured Yahiko. Seeing this, Nagato activated his Rin'negan, and killed the Rock Chunin, 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. After three years, Jiraiya felt they were strong enough to fend form themselves and told Nagato, he will see him again when he has grown into an adult. Jiraiya believed Pein to have died with the others under unexplained circumstances, but has told Konan 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 sort of god in that village. When he, and Madara Uchiha, founded Akatsuki is unknown but he 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.

Akatsuki's Goal
For the most part, Pein has kept away from active Akatsuki business, only revealing himself whenever they have captured a tailed beast and even then he only appears as a shadowy illusion. However after Deidara's suicide, Pein was ordered by Tobi that it is his mission to now capture the Nine-Tailed Demon Fox. Before the mission could begin however, Jiraiya infiltrated the village to try to get more information on the Akatsuki. After feeling this threat because it disturbed his rain, Pein sent Konan to deal with it while he changed bodies. When Jiraiya promptly defeated Konan, Pein appeared with murderous intent, his eyes set on Jiraiya.

Discrepencies in Identity
It is mentioned at various points from chapter 370 and onward that Pein's backstory is shrouded in mystery, several of the Hidden Rain village memebers claiming he doesn't exist, whilst others have different beliefs about who he is. Some specualte that he is from the Fuuma clan, which holds true to one of his bodies. It could be that Pein's backstory is so shrouded due to each person that makes up Pein as an entity have had their backstories confused over time. The only definate things are that he ended a civil war in Amegakure and kiled the leader, Hanzo, his family, firends and subordinates.

Abilities
Although he has not been seen in battle until his battle with Jiraiya, Konan states that Pein has never lost a fight. The only named ability he is seen using, the Shapeshifting Technique, allows him to clone his subordinates using human sacrifices that they control and can use to engage enemies without risking their own lives. The clones formed are perfect copies of the original, possessing any unique genetic traits or weapons they may possess. The clone's abilities are proportionate to the amount of chakra, given to the clone. Pein has also displayed the ability to detect the movements and chakra levels of people traveling within rain, as well as the ability to control rain, such as stopping it or keeping it going for long periods of time. Pein has several bodies, apparently for different purposes, that he has stored away. He can apparently switch these bodies at will, as he switches to one body solely to kill an intruder. In all Pein has six bodies ready for use, and of the two bodies he has been seen in, the only consistent physical characteristics are a large number of piercings and his Rin'engan eyes. When he was first trained by Jiraiya, he learned. At some point, Pein learns the Summoning Technique, and appears to have made several contracts as he summons a giant crustacean, an armored chameleon, a cerberus-like creature, a large bird and probably more all with the Rin'engan.

His most important technique in regards to the Akatsuki is the Illusionary Dragon Nine Consuming Seals. When used with the aid of all surviving Akatsuki members, they begin the three day trial to forciably extract the tailed beasts from its host and forces it into a statue. There seems to be a limit on which tailed beast they can seal at once however as they are unable to seal the demon fox without sealing the other beasts as it would destroy the statue, possibly freeing all the captured beasts. When all six bodies are together he calls it "Pain Rikudou" or Six_Paths of Pain. Each one of Pein's bodies appear to have a special ability, only two of which have been seen, one being able to absorb ninjutsu and the other capable of using many summons, all of which with the Rin'negan. The long haired body that is used for summoning is also shown to wield a sword like weapon that disrupts chakra flow. The body he uses most of the time when not in battle has been recognized as Yahiko's body by Jiraiya, even though Pein insists that Yahiko is dead. One of Pein's body's interestingly enough, is often shown with his eyes closed (shown at second from the right), which could be due to blindness or some other reason to have the eyes closed often.

Jiraiya also remembers fighting the summoner Pein before who was once a Fuuma clan menber. All of Pein's bodies have been recognised as shinobi Jiraiya has encountered before, shortly after the Great Toad's prophecy.