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.
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.
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.
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 Pein(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 Pein'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. Pein simply answered "Pein 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 Pein'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 Peins dog-piled him, crushing his throat in the process.
Pein 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 summon's 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, Pein praised his former sensei saying that Jiraiya would had won if he knew his secret. Pein then announces that he's aware of Zetsu's presence. One half of Zetsu wonders why it took Pein so long, but the other side of Zetsu interjects that he was fighting Jiraiya.
Pein is later shown sitting near Konan and Madara. Madara asks why Pein hasn't gone after the Nine-Tails yet, Pein said that he had an unexpected guest. Madara then mocks Pein, saying that Jiraiya must had been very powerful if the "invincible" Pein had trouble with him. Pein 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 Pein 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. Pein then signals to Konan that it's time to go to Konoha and reveals his new body, a girl.
Pein 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 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 located Iruka and asked him where Naruto was, but he refused to answer. Pein 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, but he dodged and created a wall behind Deva to corner him, but 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 Pein'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 killing 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 interrogated two other ninjas, but discovered Konohamaru and went to capture him, but Ebisu attacked Pein 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. Konohamaru single handedly defeats Hell Pein with a Rasengan taught to him by Naruto which surprises Ebisu. Meanwhile Deva Pein talks with Tsunade, it is reveald that none of the 6 bodies of Pein are his. Before Shizune, Ino, Inoichi, and the ANBU go to tell Tsunade, Human Realm attacks and captures Shizune, threatening to kill her if anyone tried to move. Human Realm then feeds the information off of Shizune, which reveals the location of Naruto and Deva Pein reveals to Tsunade that he knows where Naruto is and uses Human to seemingly remove Shizune's soul. He and Tsunade argued some more which made him angry; Beast Pein quickly left the village and summoned the other bodies and Konan, excluding Deva Pein, and told Konan that he's going to do "that," which Konan advised against since it would shorten his life. The Pein bodies then fall over and Deva rockets into the sky, then pushes most of Konoha to the ground using a move called Shinra Tensei.
Shima and Fukasaku became aware of what was going on in Konoha and took action, Shima then summoned Naruto, Fukasaku, Gamakichi, Gamabunta, Gamaken, and Hiro. is brought back and Pein is no longer set to leave. Hell repairs the busted up Asura. Beast then summons the other Realms of Pein next to Deva. Asura is sent to kill Tsunade in her weakened state while splitting her chakra through Katsuya to heal many injured but is is destroyed by a single blow from Hermit Mode Naruto.
Beast summons a rhino that charges at Naruto, but Naruto grabs it and throws it into the air. Animals summons two more, a yak and a dog, but Naruto uses Shadow Clones that send them into the air with the rhino using Oodama Rasengans, where they're taken down by Gamabunta, Gamaken, and Hiro. Hungry Ghost then launches at Naruto, Katsuyu warns Naruto that it'll absorb jutsus so Naruto strikes it; while it appeared that Hungry Ghost evaded, the natural energy around Naruto extends the range of Naruto's strikes and defeated him. Naruto then creates the Rasenshuriken and throws it at the 5 remaining Peins, and all but Human manages to avoid it. Beast lauched a giant bird at Naruto but he dodges it , meanwhile Gamabunta and the other two are dealing the the dogs that keeps multiplying. Shima uses Dust Cloud to blind all of the Peins while Naruto works in combination with Gamabunta to take down Animal Path with a Twin Rasengan inside of Gamabunta's mouth. With Animal gone, the multiplying dog summon dispersed. But Naruto finally ran out of enough nature chakra to sustain Hermit Mode and reverts to an exhausted normal state and is sprung upon by Deva, with the two exchanging blows in hand to hand combat. It's revealed that Naruto left Shadow Clones back at Myouboku mountain using Hermit Mode, and Fukasaku reverse summoned one so that it would allow Naruto to use Hermit Mode once again upon poofing. Naruto broke Deva's chakra spike and, once again in Hermit Mode, kicked Deva aside. Naruto then created another Rasenshuriken and threw it at Deva, but Hungry Ghost reappeared and absorbed it, Naruto realized that Hell revived it. Naruto then hit the ground with a Rasengan to create a dirt cloud and threw another Rasenshuriken, but it transformed into Naruto and tackled Hungry Ghost, allowing the real Rasenshuriken to hit Deva but his power finally returned and deflected it. Naruto then put his elbow over Hungry Ghost's face as a Shadow Clone dived at Hell with Twin Rasengan.
The Shadow Clone dives at Deva as Naruto is about to crush Hungry Ghost's head, but Deva pushed them back. Gamabunta, Gamaken, and Hiro leap in to help, but Deva also pushes them away. During this time, Fukasaku tells Naruto to use a genjutsu, which Naruto says he can't do, so Fukasaku and Shima volunteer but say they need time to gather enough natural energy to do it. Deva then pulls Naruto towards him and Hungry Ghost grabs him and drains the natural energy from his body, returning him to normal. Shima and Fukasaku tell Naruto to hang on.
While being forced to remain still, Naruto starts to absorb natural energy and Hungry Ghost suffers "toad petrification," and literally breaks free from his grip. Deva sees Fukasaku and Shima preparting their genjutsu and pulls Fukasaku towards himself and stabs him with his spike, then throws him at Naruto and then proceeds to slam Naruto into the ground and stab his hands. Pein's rods are disrupting Naruto's chakra control and he's having a hard time moving, so Pein decides to answer Naruto's question to his cause. He reveals coming from a small country ravaged by the wars of ninja. Pein blames it all on a cycle of hatred and the failure for people to understand one another. He forces Naruto to see they are both following Jiraiya's tutelage along different paths. That the are both trying to bring justice through revenge which goes along the cycle of pain. Pein shares that the combined power of the tailed beast will create an ultimate weapon. Pein will use that weapon to invoke great fear and pain of loss that will temporarily cease all war. He knows for a decade or less there will be true peace before it all starts over again. Pein is finally shown in his true form as Nagato with Konan by his side. Nagato has used up nearly all his chakra but wont stop as his way of achieving peace is near.
Hinata rushes in to aid the incapacitated Naruto, confessing her admiration and love for him, but Deva repels her and stabs her. Naruto goes berserk and transforms into his six-tailed form. He rushes at Deva whom tried to repel him, but Six-Tailed Naruto stabs his tails into the ground to ground himself and Deva gets pushed back instead. Six-Tailed Naruto pounces on the downed Deva and starts to charge his chakra blast, but Deva uses Heavenly Attraction to slam Six-Tailed Naruto into the ground, where he drops his chakra ball and it explodes underground, with Deva barely surviving. Deva then runs off closer to Nagato, whom says that Deva's close enough to use Heaven Earth Star, a technique Rikudou used to create the moon, however Deva's is far inferior. He concentrates and charges a ball in his hands which he throws into the air, and it starts pulling everything towards it, trapping Six-Tailed Naruto in a prison of rubble. However Naruto sprouts more tails, emerging from the rock as a giant, skinless version of the 8-Tailed Kyuubi.
Naruto however reverts back to normal and enters Sage Mode, however the miniature moon starts to crumble due to the chakra strain on Nagato. Deva attacks Naruto with an arm spike, but Naruto broke off the spike and kicked Deva away. Naruto uses Rasenshuriken and throws a smoke bomb, Deva deflects it, but then comes another Rasenshuriken and some rocks next to Deva turn out to be Shadow Clones which try to hold Deva in place, but Deva stabs them and leaps out of the way. Suddenly, all the rocks around Deva turn out to be Shadow Clones and they leap at Deva, but they run out of time and Deva pushes them all away. Naruto then had other Shadow Clones throw him and he rammed into Deva with the Rasengan. Naruto then stabbed himself with one of Pein's spikes and traced the chakra signal to Nagato's location and went to meet him. While there, Nagato stabbed Naruto and tried to control him, but couldn't. Naruto wanted to know how Nagato became what he is, so he started to tell his story.
As a child during the second great shinobi war, Nagato and his parents hid inside of their home instead of fleeing. Leaf ninjas came into their home, not knowing the family was still there, looking for supplies. Nagato's father attacked, prompting a retaliation from the ninjas believing them to be enemies. After the parents were dead, the ninjas realized what a mistake they made, and Nagato's unconsciously killed them. He would then become homeless and struggle to survive along with a dog he found, until he met Konan and Yahiko, and they all helpled each other work and steal to survive. They came to witness the battle between Hanzo and the Sannin, where a stray paper bomb killed their dog. Yahiko decided that if he was going to make the world better, he had to get stronger, and the orphans sought out someone powerful to train them... they sought out Jiraiya, but Nagato hated Jiraiya because he was a Leaf ninja. When a stray Rock ninja attacked Nagato and Yahiko, Nagato blacked out again and killed the Rock ninja. Nagato felt remorseful and scared of his power, but Jiraiya gave him words of wisdom and Nagato quickly formed a bond with Jiraiya.
Jiraiya trained the children, and helped teach Nagato to control his Rinnegan. After three years of training, Jiraiya left, leaving them to try to obtain peace. Yahiko became the leader and they fought against all sides of the war, he was a radical thinker and he quickly gained many followers, wanting peace. Hanzo eventually came to Yahiko, saying that he can use them to form treaties with the warring villages. When Yahiko and Nagato showed up to the assigned meeting place, they found Hanzo along with Danzo of the Leaf village's Root and that they came to an arrangement; Hanzo would help Danzo become Hokage, and Danzo would help solidify Hanzo's leadership of the Rain village, but in order to do this they had to get rid of Yahiko's influence. Yahiko and Nagato found that Hanzo had their companion, Konan, hostage and threatened her life if Nagato didn't kill Yahiko. In order to save his friends, Yahiko committed suicide. At which point, Hanzo ordered his soldiers to kill Nagato aswell. They threw kunais, but Nagato repelled them with Shinra Tensei and leaped after Konan, Hanzo backed away and revealed his trap, Nagato's legs were covered in paper bombs but Nagato remained standing after the blast, despite his legs in horrible shape. Nagato then summoned the Heretical Demon Statue, at which point spikes extended from it and pierced Nagato's back which whithered him, and an energy came out of the statue's mouth removed the soul of everyone it hit. Hanzo however was not that easy to hit and escaped.
After the Heretical Demon Statue was unsummoned, the spikes remained in Nagato's back.
Nagato wanted to know what Naruto's answer was to bring peace, and Naruto replied that he'd believe in Jiraiya's teachings. Nagato mocked him, but Naruto pulled out Jiraiya's first book. Nagato remembered reading it, and in it there was a note from Jiraiya, thanking Nagato. Nagato saw himself as he once was in Naruto and decided to leave his faith in Naruto to bring peace to the world, and remembering Jiraiya, Nagato brought back everyone that he killed at the cost of his own life.
Nagato was brought back to life by Kabuto using Orochimaru's Impure World Resurrection jutsu along with many other deceased warriors, making them and Nagato his immortal servants. After allying with Madara, Kabuto sent out his zombies to fight in the third ninja world war.
He and Itachi, whom was also resurrected after his battle with Sasuke, were sent out to find Naruto and Killer Bee before Madara did and succeeded. While reluctant to fight, they are forced by Kabuto to fight and defeat the last Jinchuuriki. Itachi made the first move using Grand Fireball which Bee used Samehada to counter, but Itachi leaped at them and Naruto intercepted him. Nagato then tried to use Bansho Tennin on Naruto, but Naruto countered that using his Kyuubi powers. Nagato then summoned, riding on his bird while Naruto's forced to fight the dog, while Bee is forced to fight Itachi. Itachi managed to use Shisui's eye that he implanted into Naruto to break him of Kabuto's control, allowing him to help Naruto against Nagato. Kabuto then erased Nagato's mind and had him attack, wanting to get Shisui's eye. Nagato used Shinra Tensei and then went after Bee, but Bee used his V2 and tackled Nagato only to have his Bijuu chakra absorbed, restoring Nagato's physical condition and pushed Bee aside, then used a summon to restrain Naruto while he used the Human realm's power. Naruto resisted getting his soul removed and Bee tried to surprise Nagato, but the chameleon saw him coming and Nagato restrained him with the Asura power. Right before Bee got a laser in the face, Itachi blinded Nagato's summons and surprised Nagato, saving Naruto and Bee. Nagato then tried to use Chibaku Tensei and Naruto thought they were doomed, but Itachi explained that everything has a weakness and together they attacked Chibaku Tensei's gravitational core, destroying it, and Itachi appeared out of the dust and stabbed Nagato with the Totsuka sword. Before he was sealed, Nagato told Naruto that he's the third part of the trilogy; Jiraiya was the first and was a masterpiece, himself was the second and was garbage, now it's time for Naruto to be stellar and wrap everything up.
Each of Pein's bodies are deceased shinobis controlled by Nagato using his chakra via rods pierced on each corpse (which they can use as weapons). All of Pein's bodies possess their own unique ability derived from which of the six realms they represent.
Deva Realm: Was once an auburn haired man named Yahiko, Nagato's friend. He was once spiteful and wanted to become a god and make the world suffer as much as he has, but was swayed by Jiraiya's teachings of peace.
Power: Has gravitational-like control, this allows the Deva Realm to push things away and attract them. It has also shown limited flight and to extend it's gravitational power outside of it's body to attract mass. However normal uses of it's ability forces it to recharge for 5 seconds between use, adding more power takes him longer to recharge.
Asura Realm: Was once a puppet master, hinting that he was from the Sand village. He fought in the 2nd ninja world war to make money.
Power: Aside from being very strong, it's able to alter it's body to form various weaponry, taking on a cyborg-like appearance. Can also alter it's body to grow additional arms and faces.
Human Realm: Was once a Ninja Academy teacher from the Waterfall village. He was a peaceful man with blue hair and was very quick.
Power: This body specialized in reading peoples' minds by grabbing their heads and can kill them in the process. It also appears to be the fastest and one of the strongest.
Animal Realm 1 & 2: The first Animal realm was a green haired ninja from the Fuuma clan and was quite ruthless. The second was a dead girl that was brought to Nagato, nothing is known about her.
Power: This body is able to summon giant beasts to it's aid, it's also able to summon the other Pein bodies aswell as Konan.
Hungry Ghost Realm: Was once a Grass village ninja that fought in the 2nd ninja world war, he was unable to farm his land because of the war. He had brown hair and a short temper.
Power: This body is able to absorb ninjutsu into it's body as well as siphon chakra directly from ninjas from prolonged contact. It is however weak against taijutsu.
Hell Realm: Was once an aging religious man with dark gray hair that preached to onlookers.
Power: This body is able to reanimate the other Pein bodies when they're killed, and can revive the recently deceased. It's also capable of discerning when someone's telling the truth and can rip out their tongue when lying.
Nagato possesses the Rinnegan, the third eye doujutsu which grants Nagato mastery of all six chakra types allowing him to use potentially any jutsu. Aside from the Six Paths of Pein, other jutsus used by Nagato are: Gale Wind Palm, Fierce Raining at Will, Heretical Demon Statue, Heretical Demon Spikes, Nine Mystical Dragon Seal, Lit Apparition, Mirrored Surface Attacker, and Shape Shifter.