Nagato

is the recognized leader of Akatsuki and is 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, Pain takes orders from Tobi, who is actually Madara Uchiha. In addition to acting as Akatsuki's leader, Pain was the leader of the winning faction in the Land of Rain's latest civil war.

Background
He is at first believed to be a boy named, who, like Konan and Yahiko were 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 chunin, 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 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.

Pain has since led one side of the Amegakure civil-war and took over the village, he has become a greatly respected leader in that village. The members of Pain's faction wear their Amegakure forehead protectors with a scratch through it the way the full members of Akatsuki do, despite the fact that none of them, including Pain, are actually rogue ninja, as the scratch symbolizes.

Personality
As a child Nagato was a sensitive but kind boy, prone to crying, and was traumatized by the idea he had killed another man, even to save his friend Yahiko. Scared and unsure of his place in the world, he desired to help those he cared about, but never knew how. Nonetheless, he became a talented and gifted student, mastering every technique Jiraiya taught him.

As Pain, his personality is very different having become a calm, serious, aloof, and detached man. Apparently believing his childhood trauma had enlightened him to the true meaning of pain and suffering, he now believes himself a deity and evolved beyond a mere human. He now seeks to show the world the meaning of suffering by using an ultimate weapon to deter future wars by means similar to "mutually assured destruction". He shows no moral qualms about his actions. He is willing to kill his own teacher in cold blood and brutally execute all of Hanzō's friends and family to ensure the Amegakure's compliance to his takeover. He even goes so far as to proclaim himself a 'god of peace' come to guide the world to maturity through pain.

Nonetheless, he can be quite respectful, particularly to the fallen. Given Akatsuki members' frequent bickering, he often restrains them and encourages better relations between the other members, even suggesting they mourn Deidara after his passing. After his battle with Jiraiya, he holds a moment of silence for his former teacher out of respect for his power.

Pain is also very respectful and kind to his childhood friend, Konan, who has been declared his "Goddess". He was shown protecting her without request or hesitation from Jiraiya before his battle with his former teacher. She apparently is the only member of Akatsuki, aside from Madara, that is allowed to address him by name.

Akatsuki's Goal
For the most part, Pain 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, Pain was ordered by Tobi that it is his mission to now capture the Nine-Tailed Demon Fox (This for unknown reasons drew an emotional response from him). 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, Pain sent Konan to deal with it while he changed bodies. When Jiraiya fought Konan, Pain appeared with murderous intent, his eyes set on Jiraiya.

Fight with Jiraiya
During the first half of his battle with Jiraiya, Pain fought the Sannin off with unique summons. It wasn't until Jiraiya activated Hermit Mode and summoned two toads to help him fight did Pain reveal two more of his bodies and quickly began to fight Jiraiya back. Jiraiya attempted to bring down all three of the bodies using the toad elders to perform a Genjutsu, then pierced each body through the heart with a giant sword. When Jiraiya prepared to go back to Konoha, Pain reappeared and attacked him, cutting off his left arm. When Jiraiya looked back up, he looked at the Six Paths of Pain, and all six bodies attacked. Not long after, Jiraiya managed to kill the long haired body of Pain, only to have his throat crushed by one and then be impaled by all five. As Jiraiya died, he sent the message of Pain's identity. Though the toad escaped, Pain called for Zetsu to come out and filled him in on his order to hunt the Nine-Tailed Demon Fox.

Hunt for the Nine-Tails
After the fight, Madara returns to inform Pain of Sasuke and Team Hawk going after the Eight-Tailed Beast (something Pain being doubtful that they could accomplish), and orders Pain to go after Naruto fast because Konoha knows he killed Jiraiya and it makes it harder to get to Naruto. When Madara leaves, Pain prepares to set out to Konoha and reveals a new body, once again completing the Six Paths of Pain. When the six bodies and Konan are about to leave, Pain, with the body of Yahiko, tells her to spare no one. When they finally arrive in Konoha, they kill a patrol of ninja and Pain quietly says that they will unleash pain upon the world. Beginning his invasion, Pain sends his Animal realm through the barrier surrounding Konoha for misguiding the villagers about their numbers. Once inside, he summons the other bodies of Pain. The Demon realm body uses his strange arm flaming arrow technique to destroy the surrounding buildings. Elsewhere the Human realm grips the head of a Leaf ninja and senses that the man does not know the demon fox's location. He pulls out the man's soul and the body collapses. Meanwhile,the Deva realm ties to interrogate Iruka about Naruto's wherabouts, but upon refusal tries to kill him. Kakashi intervines and both Pain and Kakashi start battle.

Abilities
As the leader of Akatsuki and one of the two sides of Amegakure's Civil War, Pain is an extraordinarily powerful ninja; his partner Konan confidently stating that he has never lost a fight. He was able to single-handedly defeat and overthrow the former Rain village leader Hanzō (who was more than a match for all three Sannin during their younger days combined) and made short work of Jiraiya after unveiling all six of his bodies.

Pain has been seen using the Shapeshifting Technique, which allows him to clone Akatsuki members using human sacrifices that they control and can use to engage enemies in place of themselves. 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.

His most important technique in regards to Akatsuki operations is the Illusionary Dragon Nine Consuming Seals. With the other members of Akatsuki, this technique begins a three day trial to forcibly extract the Tailed Beast from its host and forces it into a giant statue. There seems to be a order on which Tailed Beast they can seal at once 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.

Part of Pain's huge power stems from his Kekkei Genkai, Rinnegan eyes. This was originally possessed by the Sage of the Six Paths, the world's first ninja and the founder of modern Ninjustsu. The Rinnegan's abilities are largely obscure but it does allow the user to use all five types of elemental chakra, as well as an unknown sixth element, an ability no ninja without it can possess.

It also enhances his vision in a similar manner to the Hyuga's Byakugan, allowing him to see through solid objects and sense the chakra of barrier techniques. The eyes also seemingly grants him the abilities of the Uchiha's Sharingan eyes, that allows him to partially, if not, completely foresee the movements of the opponent.

Six Paths of Pain
The most prominent fact about Pain is that he is not a single entity, but six individual bodies all acting together with one mind and will. He calls this the. Normally, he operates out of a single body and keeps the others stored in sealed room within a strange machine. The only common feature shared by these bodies is their bright orange hair and Rinnegan eyes. Each also has a vast number of body and facial piercings of various shapes, sizes, and patterns. If you look closely enough, each body somewhat resembles another Akatsuki member (1st body: Tobi, 2nd body: Deidara, 3rd body: Hidan, 4th body: Orochimaru, 5th body: Kakuzu, 6th body: Kisame, 7th body: Konan).

Each one of Pain's bodies have a single special ability and defined purpose, and he coordinates his multiple selves together via their eyes. Each body can see and sense everything that the other bodies can, giving him a maximum of six fields of view, allowing him to co-ordinate powerful multi-directional offense and defense with incredible speed and precision. They also all carry strange black spear-like weapons that can disrupt a target's chakra on contact. Most disturbing, the bodies can apparently recover from even fatal injuries providing several other bodies survive. During battle, Jiraiya realizes that all the bodies are in fact those of other shinobi that he encountered on his travels although how they came to be part of Pain is still unknown. Also during the arc of Pain in konoha, Shizune (who is holding a black piercing from the old summoning body) explains that the device in her hand picks up high chakra frequency and that it was picking up chakra signals from the piercing. Later, Tsunade gives a theory that the bodies of pein move to what chakra signals they receive or that it is a way for chakra to connect them together. This could also put the possibility for someone else to be controlling the bodies from far away. Pain refers to his bodies as Paths and later on as Realms. Although he has six selves he appears to prefer using one body to give orders and co-ordinate his actions. According to Jiraiya, Nagato's original body apparently isn't with these bodies, but where it is, or if it even exists, is unknown.

Pain's first observed body is that of his childhood companion Yahiko, possessing medium length spiky hair, seven piercings on each ear and a metal bar piercing through each ear, three piercings through the side of his upper nose and one spike stud on each end of his bottom lip. This body is apparently his preferred form for interacting with others since it has participated in all sealing rituals and was seen in several flashbacks by Rain village members. This body has the ability to control rain, and can conjure and stop it at will, even maintain it for long periods of time. This is apparently tied into his mood. In addition he can detect the movements and chakra levels of people traveling within the rain, making it difficult to infiltrate the Hidden Rain village by stealth. During his fight with Kakashi he displayed a telekinetic ability that allowed him to move objects or people towards him or away from him.
 * First Body (Yahiko) -

Jutsu
 * Rinnegan
 * Fierce Raining at Will
 * Five Seal Barrier
 * Shapeshifting Technique
 * Lit Apparition Technique
 * Illusionary Dragon Nine Consuming Seals

The third body is a fat, bulky man with six spike stud piercings covering his entire bottom lip, two studs vertical on the front of his nose, two spike studs one on each cheek, a metal bar going through each ear, and a stud on his shoulder one on each side close to his neck. He is a defensive body, somehow capable of absorbing any Ninjutsu related technique, even an over-sized Rasengan and a combination elemental attack with no sign of injury. He can also create a defensive bubble like shield capable of absorbing attacks from any direction. His hairstyle bears some resemblance Hidan's. Originally this body was from Kusagakure.
 * Third Body -

Jutsu
 * Rinnegan
 * Sealing Technique Absorption Seal

The fourth is a tall slender man with very long loose hair, a diagonal bar though his nose, two studs vertically on each cheek, two studs horizontal from each other on his upper chin, and a stud on his shoulders near his neck. Jiraiya damaged this bodies eyes early on in his battle so its abilities went mostly unseen but attacked Jiraiya with Taijutsu at first encounter. More recently however it has shown the ability to read minds by touching another head, and then rip out the soul apparently killing the victim. This body was originally from Takigakure.
 * Fourth Body -

Jutsu
 * Rinnegan

The fifth is a tall bald man with a very unusual body shape, possessing a very thick neck, a big square shaped jaw, with a large ring piercing on his nose, spike studs all around his head, three studs on the top and bottom of each of his arms, and an enormous spike stud on his chin. Later in the series, the studs on his head turn into spikes and he gains two vertical spikes on each upper cheek. He was initially shown to be perpetually smiling. He has great physical strength and can detach and fire his body parts like a missiles for long range attacks, capable of shattering stone on impact. His ability seems to be based on the weaponry and the same human puppetry made by Sasori. In the latest chapter it is shown that this body actually has six arms, three faces (each showing a different emotion: happy, neutral, and angry), a scorpion like tail, and strongly resembes an actual puppet. He can also release an large explosion from his head. This body is also implied to have blown off Jiraiya's arm when he ambushed him. This body has recently been stunned by Kakashi, then crushed by Choza Akimichi and Choji Akimichi.
 * Fifth Body -

Jutsu
 * Rinnegan
 * Strange Arm Flaming Arrow

His sixth body is a stocky muscular man with a spiky mop of hair and very tall (similar in style to Kisame Hoshigaki's), triple bar ear piercings, a stud on his upper nose, a stud on his shoulders near his neck, and a row of studs diagonally down each cheek. In contrast with the fifth body, this one is shown to be constantly frowning, In the latest chapter, this body displays what could be a Genjutsu ability that he used to interrogate a leaf ninja. This could also be a statue summoning with the power of the Rinnegan as the flames closely resemble Amaterasu.
 * Sixth Body -

Jutsu
 * Rinnegan

Pain's newest, female-like body is the new body to replace the one lost in the fight against Jiraiya. This body has a very young appearance, with its hair tied together in a sort of onion like bun at the top of the head and spikes of hair protruding out of it. It has one stud above the nose, studs on either side of the neck, a row of studs vertically down each cheek, a stud below each stud on the neck and two studs on each forearm. either This body also bears some resemblance to Konan. So far the only attack it is seen using is its ability to summon a giant centipede, and like the body it replaced it is capable of summoning the other Pain's. This body was first shown when Pain announced to Konan that they were going to Konoha. This body can be seen as a reincarnation of Pain's second body, due it being the one used for summoning.
 * Seventh Body -

Jutsu
 * Rinnegan
 * Summoning Technique
 * Centipede
 * Other Pain Bodies

Former Bodies
His second body, distinguished by a long ponytail and large bridge piercings through his upper nose and attaching on his cheeks, one on his upper nose, and six rimming around the bottom of his face in his chin area. After being killed and examined, this body was shown to have multiple piercings on his chest as well. The appearance of this body, when first seen, was compared to that of fellow Akatsuki member Deidara. This body is a more battle orientated form. This body is a powerful summoner, capable of conjuring a massive variety of different animal summons for various different purposes, and most significantly the other bodies of Pain. Each animal summon also shares his Rinnegan eyes and various piercings suggesting that they too are under his control. Prior to Jiraiya's encounter with Pain, one of his subordinates noted that some believe Pain to have been from the Fuma clan. This is because the body was originally a man from the Fūma clan, recognized by Jiraiya as a man who had ambushed him, ending up scarred across the forehead in the process. This body was the first one encountered by Jiraiya, and was eventually killed and sent to Konoha for study. It is safe to say that this body previously held the Chikushōdō designation.
 * Second Body (Fuma Clan Summoner, deceased)

Jutsu
 * Body Replacement Technique
 * Rinnegan
 * Summoning Technique (Multiple)
 * Crustacean
 * Chameleon
 * Multi-Headed Canine
 * Panda
 * Bird
 * Yak
 * Violent Bubble Wave (Crustacean Summon)
 * Amplification Summoning Technique (Nine-Headed Canine Summon)
 * Panda Iron Wall (Panda Summon)

Trivia

 * Each body of the "Six Paths of Pain" has a designation matching each of the Six Paths of reincarnation in Buddhism: Deva, Asura, Human, Animal, Preta, and Naraka. It is possible that Kishimoto intentionally derived the designations from Buddhism, however, no connections have been officially confirmed.

Speculations
Before chapter 363 when the face of Pain has actually been fully shown, there was a theory highly popular in fandom that stated the Akatsuki Leader is the Fourth Hokage. This speculation has been recently resolved as incorrect, however even in the light, Pain's Yahiko body resembles Minato Namikaze in ways. Some fans still believe Pain is the Fourth Hokage in disguise as not to have people know who he is since Pain has multiple bodies, but this fact has yet to be proven or disproved. Another speculation is that the multiple bodies of Pain are a variant of his Shapeshifting Technique, used to split his chakra and abilities into multiple bodies.

It can also be inferred that Pain has a seventh body, because in the message Jiraiya left, it mentions that "the real one is not with them". This could mean that the head body, which could be Nagato, controls his six bodies from a distance, and as long as the seventh one survives, Pain can't die.

If you look closely at the piercings of the Pain bodies faces you can see: first body has seven piercings in both ears and six piercings in his nose (if you think it over there are only 3 piercing in the nose), second body has seven circle piercings on his face, third has body six circle piercings on his face, fourth body has six piercings under his lips, fifth has body six piercings on top of his head, sixth body has seven circle piercings on his face, seventh body has seven piercings on his face. This seems to be connected with the six/seven theme with Pain. Whether it is a clue to how the bodies work or not is unknown.