Nagato is the leader of the Akatsuki but is actually was actually a tricked victim for obito in Naruto. He has six different paths which he uses in six different bodies, all accessible through the legendary Rinnegan. His true identity is that of Nagato,a former student of Jiraiya.
Nagato grew up in the Hidden Rain Village and as a young child, his parents were murdered in front of him by Hidden Leaf Ninjas. This act awakened his Rinnegan and allowed him to kill the ninjas, although he was unaware of what happened. Now an orphan, he wandered throughout the village and nearly died of starvation until he met Konan and Yahiko, fellow war orphans. The three of them quickly became friends and worked as a trio to stay alive.
One day they stumbled across a battle between the Hidden Leaf's Sannin (Tsunade, Orochimaru and Jiraiya) and Hanzo, the military leader of the Hidden Rain Village. Yahiko was impressed by the three and decided to seek instruction on how to become a ninja from them. Konan and Nagato followed in his footsteps and they eventually were able to find them. Orochimaru suggested killing them out of mercy because, as they were orphans, their lives would only get worse and worse.
Jiraiya decided against that and chose to instruct them instead. It was during this time that he told Nagato about his desire to spread peace and understanding and Nagato took up the mantle. Eventually Jiraiya left the three and returned to the Hidden Leaf while Yahiko and his group continued down the path of peace that Jiraiya imparted them with.
As teens, Yahiko, Konan and Nagato founded a peacekeeping organization called Akatsuki (an idea came up by Madara Uchiha and gave it to Yahiko) in the Hidden Rain Village and began receive acclaim for it. Fearing that this would lead to his downfall, Hanzo and Danzo, who feared that peace would put an end to his war fueled quest to become the Hokage, agreed to setup the group and arranged a situation for all three of them to be killed. Yahiko died as a result and Nagato fully embraced the idea of war and death being the only way for peace to be achieved. Pain eventually killed Hanzo but he didn't stop with him; he killed Hanzo's family, friends, and associates as well.
Pain is an antagonist in Naruto he maid his full debut in Naruto volume 40 and he was thought to be the leader of Akatsuki but he is actually a figurehead for Tobi.
Nobody in the village knows whether or not Pain 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 Pain 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 Pain's plan is. Pain 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.
After Deidara died, Konan and Pain await on the arrival of a shadowed figure. This shadowed figure tells them of Sasuke's potential. This person then tells Pain to order the remaining members to capture their Bijuus and tells Pain to capture Naruto, but warns him of Naruto's power. Konan interjects, reminding their guest that Pain 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. Pain, 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 Pain 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 Pain used a substitution technique to escape, he then appeared riding a chameleon-like chimera. Pain 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. Pain 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 (senjutsu). Two great sage toads, Fukasaku and Shima, summoned by Jiraiya and merged onto his shoulders destroyed Pain's chameleon-like chimera. Pain summoned two of his other 5 bodies, the Hungry Ghost Realm (aka Preta Path, 餓鬼道 Gakidou) and Human Realm (aka Human Path, 人間道 Ningendou) bodies. Human attacked first but was struck aside and blinded, impressing Pain. Hungry Ghost then blocked and absorbed Jiraiya's ninjutsu. Jiraiya used another ninjutsu directed at Hungry Ghost. However, 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. Thanks to one of Rinnegan's abilities, all of Pain's bodies was able to block the "unseen" attack by seeing what the other bodies see. 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. Pain's bodies regrouped after Jiraiya's attacks and prepared to attack, but Jiraiya disappeared and Pain realized that Jiraiya was hiding in the surrounding pipes and ran along-side them, listening. He heard Jiraiya's summons croaking and chased after. Pain 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. Jiraiya trapped Human, leaving only Beast and Jiraiya.
Beast tried to summon but Jiraiya stopped him, Jiraiya then lectured him saying how he's never supposed to underestimate his opponent. Jiraiya's summons' genjutsu started to take effect and Jiraiya told him that this genjutsu paralyzes the body and mind. With Pain(s) trapped in the genjutsu, Jiraiya stabbed each of the bodies through the heart. Jiraiya then started to leave, believing the fight was over, but Pain's other bodies arrived and one attacked Jiraiya from behind a few moments later, saying that Jiraiya supposedly taught him not to underestimate his opponent, another body then resurrected the other three bodies. Jiraiya, now missing an arm as a result of the ambush, asked how they all six of them had the Rinnegan. Pain simply answered "Pain refers to all six of us."
Jiraiya escapes into a summoned frog's stomach, but Beast managed to follow him there and stabbed Jiraiya in the right arm and shoulder... Beast unfortunately was killed during the fight and was partially submerged in the frog's stomach acid, one of Jiraiya's summons then takes that body to Tsunade. It would be revealed that all of Pain's bodies are ninjas Jiraiya encountered before. Jiraiya then, no longer in Hermit Mode, left the sanctuary of the frog stomach to make sure, and that's when the 5 other Pains dog-piled him, crushing his throat in the process.
Pain had successfully impaled Jiraiya in the back with 5 spikes and was starting to leave when he realized that Jiraiya revived himself. He saw Jiraiya write an encrypted message onto one of his summons back and quickly chased after it, in the pursuit the island that Jiraiya was on crumbled and Jiraiya sank to the depths below. Although the toad got away, Pain praised his former sensei saying that Jiraiya would had won if he knew his secret. Pain then announces that he's aware of Zetsu's presence. One half of Zetsu wonders why it took Pain so long, but the other side of Zetsu interjects that he was fighting Jiraiya.
Pain is later shown sitting near Konan and Madara. Madara asks why Pain hasn't gone after the Nine-Tails yet, Pain said that he had an unexpected guest. Madara then mocks Pain, saying that Jiraiya must had been very powerful if the "invincible" Pain had trouble with him. Pain got angered by this and said that Jiraiya was dispatched and that he can go after the Nine-Tails whenever he wants. Madara then starts to leave and informs Pain that he has to hurry since Konoha will be ready for him if he waits too long, then informs them that he sent Sasuke after the Eight-Tails. Pain then signals to Konan that it's time to go to Konoha and reveals his new body, a girl.
Pain arrived at Konoha's borders and killed some guards. While assessing the walls, he used his Rinnegan to see an invisible barrier around Konoha that detects intruders, as such he decided to use Asura Realm, Beast Realm, and Hungry Ghost Realms as distractions while Deva Realm, Human Realm, Hell Realm, and Konan search for Naruto. Asura (aka 修羅道 Shuradou) then threw Beast over Konoha's wall where she summoned the other 5 and Konan upon landing, and then summoned a giant centipede to attack and Asura pulled off his arm and fired multiple rockets. Human Realm attempted to extract information from a ninja but he didn't know anything, then proceeded to kill him.
Deva Realm (aka Deva Path, 天道 Tendou) located Iruka and asked him where Naruto was, but he refused to answer. Pain was able to strike him with an arm spike, but Kakashi arived and stopped the strike and told Iruka to leave. Deva went to kick Kakashi, who dodged and created a wall behind Deva to corner him. However, Deva managed to stab Kakashi in the shoulder. Kakashi was about to Raikiri Deva's head off, but Deva's spike started affecting Kakashi and delayed him long enough for Deva to dodge and push Kakashi away with a jutsu. Kakashi crawled out of some rubble and used a jutsu against Deva, but he pushed it away and that's when Asura arrived. Kakashi and Asura started fighting, Kakashi dodged his attack and was about to strike him from behind with Chidori but Asura dodged and Kakashi noticed Deva paying close attention from a distance and remembered what Jiraiya's toad told him about Pain's eyes. Asura then leaped infront of Deva and pulled off his cloak, revealing three faces and six arms along with a blade-like tail on his back. Deva then used his power to pull Kakashi towards him, Kakashi tried to stop himself but Asura stabbed him in the chest with his tail... and poofed, it was an Electric Clone that electrified Asura and was simultaneously crushed with the arrival of Chouji, Chouza, and three other ninjas.
All six attacked with ranged weapons, but Deva pushed them all away and knocked all but Kakashi, Chouji, and Chouza unconscious. They continued to throw kunais at Deva but he started dodging them before using his ability again. Kakashi realized that Deva can't use that ability consecutively which gives them a window of opportunity, and worked out a plan. Kakashi used Groundhog Decapitation to appear below Deva and try to stab him, but Deva pushed him away. Deva was about to stab Kakashi with a spike until Chouji and Chouza tried to ram him and pushed them away, however they anticipated that Pein would do that so what they did was grab a chain that Kakashi secretly laid underground beneath Deva and held him tight and Kakashi went in for the kill with a Raikiri, however Asura somehow leaped in the way to take the hit instead. Some of the fight at this point went unseen, and Chouza took a killin blow meant for Chouji. Then while Kakashi was pinned under some rubble, Deva picked up a nail and launched it at Kakashi and left. Unknown to Deva though is that Kakashi actually used Kamui to suck the nail away and laid unconscious. Chouji came to and realized his dad was dead, but Kakashi told him to hurry and tell Tsunade Deva's power. Asura turned out to still be alive and tried to shoot Chouji with a rocket, but Kakashi used the very last of his chakra to suck the missile away with Kamui.
Hell interogated two other ninjas, but discovered Konohamaru and went to capture him, but Ebisu attacked Pain so that Konohamaru could escape... he didn't though, and came to his teacher's aid. Meanwhile, Beast is fighting Ibiki and some Anbu while Deva confronts Tsunade and Hungry Ghost fights Kiba and Tsume. Later on its is revealed that the highest tower in the village of rain is actually Pain's labortory where he inserts black chakra rods into the deceased corpses. The reason he chose the tallest tower is due to the fact that it acts like a radio tower meaning in order to operate his six realms he needs a place high enough where the six bodies receive his chakra signals until now it has never been revealed what pein really looks like or what he did to his own body to acquire the six realms.
Naruto fought against all the Paths of Pain, destroying all six. After he defeated the Deva Path, Naruto stabbed himself with a chakra reciever, tracking where Nagato was located. After a long conversation between Nagato and Naruto, the former believes in Naruto and his ideals. Nagato then uses the remaining of his chakra to undo his Gedou Rinne Tensei no Jutsu to revive all the people he had killed in the invasion of Konoha. With that done, Nagato passed away.
Madara would later return to the Hidden Rain village to do battle with Konan over Nagato's body, Madara revealing that he implanted the Rinnegan in Nagato when he was born in order to develop its abilities and Maid Yahiko Form Akatsuki. He succeeded and would implant one of Nagato's Rinnegan in his left eye-socket, replacing the sharingan used to perform the Izanagi justu against Konan who later died.
Nagato was one of the bodies brought back to the world of the living by Kabuto Yakushi's use of the Summoning: Impure World Resurrection justu (Edo-Tensei). He was kept away from the war with Itachi Uchiha as he was brought back the way he died with his crippled body. Through Kabuto's body manipulation, Nagato's body's youth was restored, allowing him to use all the abilities he had spread through the paths of pain bodies at once. Although Itachi managed to free himself from Impure World Resurrection's control (through Shisui Uchiha's Mangekyou Sharingan, previously planted in Naruto), Nagato had no such method, leaving him at the mercy of Kabuto, who used him to attack Itachi, Naruto and Killer Bee.But soon Itachi sealed Nagato and kabuto revealed even if Nagato got back his mobility and restore into his youth Nagato was unable to move due to having never walk for so long .
Pain possesses the Rinnegan, the same eye technique that the first ninja and inventor of the ninja world, the Sage of the Six Paths, possessed. 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 reduce everything to nothingness.
All of Pain's bodies possess their own unique Jutsu derived from which of the six realms they represent, aside from basic ninja techniques such as Substitution and Body Flicker. They also share a couple abilities, such as spikes that extend from their right forearms and linked vision.They were linked through corpses by using charka receivers
Deva Path: Gravity manipulation,channeled through the body of Yahiko ,Nagato's best friend.
Asura Path: Cyborg Body (Super Strength, Chakra Propelled Boots, Launcher Limbs, Shockwave Cannon in Head),channeled through a body of a puppeteer
Human Path: Mind Reading, Soul Removal,channeled through the body of a teacher
Preta Path: Chakra Absorption,was channeled through the body of an obese grass ninja
Naraka Path: King of Hell summoning (Interrogating and Resurrection purposes),was channeled through a body of a priest.
Outer Path: The Seventh Path used to control and create the six paths of pain,Use the Samasra Heavenly of life tenchique to bring back the dead,and Charka Chains to bid and restrict enemies.
He has used other jutsus ambiguously, so it's unknown which if any of the bodies are credited. These are: King of Hell statue, Lit Apparition, Mirrored Surface Attacker, Nine Mystical Dragon Seal, and Shape Shifter. He has also displayed two abilities that have yet to be explained, those are possession of others and resurrecting his deceased bodies.Nagato himself is the outer path and sevenith pain as he can control the six pains and bringe back people from the dead back to life.
Through the properties of the Summoning: Impure World Resurrection jutsu (Edo-Tensei), Nagato's body is restored to full health. Nagato's full mobility is restored, allowing him to use all six paths of pain at once without the need for other bodies. Under Jiraiya's training, Nagato also learned all six elemental chakra affinites, fire, water, lightning, earth, wind and yin-yang (physical energies - spiritual energies).