Nagato

was an orphan from Amegakure and a student of Jiraiya who grew up during the Second Shinobi World War. Orphaned by the conflict, Nagato banded together with his fellow war-orphans to form Akatsuki, an organisation whose goals were to stop the endless cycles of death. After his friend and leader, Yahiko, was killed for preaching peace, Nagato became convinced the world would never stop fighting willingly unless it knew what true pain is. He adopted the alias of and began leading Akatsuki in an effort to force the world into a state of peace through fear of destruction by Akatsuki's hand.

Background
When Nagato was a child, Madara Uchiha claims to have transplanted his own eyes into the young boy without his knowledge. Nagato lived with his parents in a village somewhere on the outskirts of Amegakure. One day, during the Second Shinobi World War, two Konoha shinobi attempted to find some rest and food in their thought-to-be-abandoned home. Believing that the shinobi were there to kill them, his parents died during the ensuing chaos in their effort to protect Nagato, as confused and shocked, the Konoha ninja mistook them for enemy shinobi. After witnessing his parents death, Nagato in his grief used the Rinnegan for the first time and killed the assailants. Nagato would eventually come to regard this as the first of two great sources of pain in his life, only later realising that it was him who had killed the two shinobi.

The orphaned Nagato wandered the country, travelling from house to house alongside a dog named Chibi, begging for food. Eventually, Nagato started to starve and later collapsed, which lead to him being found by Konan, who gave him a loaf of bread before taking him to the hideout she and Yahiko had made their home. At first, Yahiko was reluctant to have another mouth to feed, but reconsidered having Nagato hang around due to both boys sharing the dream of a world without suffering. The three then began to search for supplies, often stealing them to survive. One day, Chibi was killed in the crossfire from Hanzō's fight with several Konoha shinobi, including the Sannin, with Nagato and the other orphans later mourning the dog's death. As the war was nearing its conclusion, the three orphans encountered the Sannin themselves. Although Orochimaru intended to kill the children to put them out of their misery, Jiraiya decided to remain in Amegakure to teach the trio how to protect themselves.

Soon after Jiraiya began living with the orphans, Nagato and Yahiko were attacked by a chūnin from Iwagakure. The need to protect his friend caused Nagato unknowingly resort to his Rinnegan once again to defend Yahiko, killing the ninja. When Jiraiya found out about this, he decided to train them in ninjutsu. Nagato was very emotional about killing the ninja and asked Jiraiya for help so he could protect Konan and Yahiko. Jiraiya's response was for Nagato to grow up and to use his eyes to find the peace that they both desired for the world. Three years later, the orphans had become competent ninja, so Jiraiya returned to Konoha.

Over the years, news of their exploits would reach Jiraiya, often consisting of the death of someone who opposed them. Eventually, he received word that they had all died. In truth, Nagato, Konan, and Yahiko began a quest to find peace by forming an organisation called Akatsuki with Yahiko as its leader. They became full-fledged Amegakure ninja and gathered followers who shared their philosophies as well as their dream of an end to all conflict. At some point, Obito Uchiha and Zetsu found Nagato, with Obito introducing himself as Madara Uchiha. The trio had their doubts about the masked man actually being Madara, but Nagato became interested in his plans after hearing "Madara" mention the Rinnegan and what he could do with it.

Fearing that Akatsuki would become a threat to his regime, Hanzō schemed with Danzō of Konoha's Root to eliminate its three leading members by making it seem that Hanzō wanted to discuss peace. Once the trap was sprung, Hanzō placed Nagato in a position where he had to kill Yahiko with a kunai, otherwise Konan would die. Before Nagato could take either option, Yahiko forcibly impaled himself onto the kunai that was placed in Nagato's hand, sparing him from making such a horrid decision himself. In his final moments, Yahiko told Nagato to survive as he believed him to be the saviour that Jiraiya spoke of. The death of his friend marked the second great pain of Nagato's life.

Devastated as he retrieved Konan along with Yahiko's corpse, a furious Nagato launched an attack on Hanzō's men. After summoning the Demonic Statue of the Outer Path and becoming emaciated from the numerous black rods that it embedded in his back, Nagato slaughtered everyone except Hanzō, who used a trap to cripple Nagato's legs. Becoming the new leader of Akatsuki, now going by the name of "Pain", Nagato severed his ties to Amegakure and resolved to show the world what the meaning of pain is.

Devising a means to regain movement by converting Yahiko's body into the first of his Six Paths of Pain, the Deva Path, Pain led rebelling forces in the Amegakure civil war and took control of the village by assassinating Hanzō. Concealing his true body in the shadows, and becoming a "god" to Amegakure's people, Pain solidified his leadership by systematically killing anyone who had ties to the former leader, from friends and family to ambassadors from other ninja villages. At some point during this time following Yahiko's death, Nagato fell under the command of Obito Uchiha and Akatsuki was reformed into a criminal organisation through his influence. Nagato would continue acting as the groups leader while Obito stayed behind the scenes.

Personality
As a child, Nagato was a sensitive, kind boy, prone to crying, and was traumatised by the idea of killing others, even if it was 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. He was consistently respectful and kind to Konan, who he claimed to be his "angel" in Amegakure. He was shown protecting her, without request or hesitation from Jiraiya before his battle with his former teacher. Apparently, she was the only Akatsuki member that addressed him by name. He was aware of Konan's feelings towards Yahiko and left them alone to have personal time together.

As an adult, after losing Yahiko, his personality became very different, having become an aloof, stolid, and serious man. Apparently believing the traumas he experienced in his youth had enlightened him to the true meaning of pain and suffering, he considered himself a deity, and believed he had evolved beyond a mere human being. He sought to show the world the meaning of pain by using an ultimate weapon to deter future wars, by means similar to "mutually assured destruction", and showed no moral qualms about his actions. He was even willing to kill Jiraiya, his former sensei, to ensure the completion of his plans. He even went so far as to proclaim himself a "god of peace", that had to guide the world to maturity through pain. Finally, he felt that no-one could understand true peace unless they understood "true" pain, something his childhood friend Yahiko believed. Minato Namikaze believed Tobi to have been using this philosophy in his favour, in order to manipulate Nagato.

Nonetheless, he was seen to be quite respectful, particularly to the fallen and the dead. Given the Akatsuki members' frequent bickering, he often quelled them and encouraged better relations among members. He even suggested that they mourn for Deidara after his passing, and reprimanded Kisame for calling Hidan and Kakuzu the "Zombie Combo". After his battle with Jiraiya, he held a moment of silence for his former teacher, out of respect for his power. He also told Kakashi that he was honoured to meet him during his invasion of Konohagakure. However, Nagato has no respect for people to have lost their convictions such as Hanzō, whom in the anime, Nagato never even bothered with a proper burial after he killed.

Because Konohagakure was partly responsible for the tragedies in his life, he held a great deal of animosity towards the village. Although Jiraiya's influence improved his opinion of the village during their time together, he eventually came to believe that Konoha profited from the tragedies of others and hated it and his former teacher.

A prevalent trait that Nagato possessed during his early years (and to some extent his adulthood) is his submissiveness and his willingness to follow the lead of others. As a child, he followed Yahiko due to his position as leader, and when he grew older he almost immediately fell for Obito's manipulation who was masquerading himself as Madara but was saved by Yahiko. After Yahiko's death, Nagato immediately turned to Obito for leadership believing him to be Madara and when pushed to the brink of defeat he was converted by Naruto within one conversation.

After his reincarnation, Nagato was shown to be kinder and carefree to the point he was even willing to start making jokes, something which surprised Naruto. His opinion of Naruto also strengthened after he last saw him, pointing out to Itachi Uchiha that he wasn't surprised that Naruto was able to advance his control over the Nine-Tailed Demon Fox since they both had studied under the same master.

Appearance
Nagato was a fair-skinned man with chin-length red hair (a colour which is a trademark of the Uzumaki clan) with his most noticeable trait being his Rinnegan eyes. As a child, his hair would regularly hang off his face blocking the view of his eyes; later only covering the right side of his face. As adult, Nagato grew to be slightly shorter than Yahiko, but after subjecting himself to the Summoning: Demonic Statue of the Outer Path, Nagato was reduced to an emaciated version of his former self with chakra receivers implanted into his back, one in each of his shoulder joints, smaller ones in his forearms and two metal-like screw under his collar bones, near his shoulder joint. Nagato uses a mechanical walker for mobility, which could fire chakra receivers for personal defence. He was the only Akatsuki member never seen wearing the organisation's uniform, until after his death, and he ceased wearing a slashed out forehead protector after defeating Hanzō. However, his Six Paths of Pain wore both in his stead. After Nagato used the Outer Path — Samsara of Heavenly Life Technique to revive all the Konohagakure citizens that had been killed during his invasion, his red hair turned white due to the overexertion of his chakra. When reincarnated by Kabuto, Nagato was left in the exact state as he died - emaciated and with white hair. The only exception were black rods that are no longer attached to his body. However, after Nagato uses his ability to absorb chakra from B's Version 2 form, this chakra seemingly revitalised Nagato's body, restoring his muscle mass, and restoring his hair colour from white back to the Uzumaki clan's characteristic red colour.

Abilities
As the leader of the S-rank criminal organisation Akatsuki, and one of the two sides of the Amegakure civil war, Nagato was an extraordinarily powerful shinobi, and recognised as the strongest member of Akatsuki. Even as a child before becoming a shinobi, he was able to kill a chūnin while protecting Yahiko. His partner, Konan, had stated that he had never lost a single battle, and that he was "unbeatable". Fukasaku stated that without understanding Pain's power, no one could defeat him, and even Obito noted that Nagato was invincible while praising Jiraiya. Nagato was able to kill Jiraiya with relative ease after revealing all six of his bodies. It was with these six bodies that Nagato led a civil war in Amegakure that not only easily killed Hanzō and overthrew his regime, but also eradicated his lineage and anyone remotely associated with him and his ideals. He was also able to effortlessly defeat Orochimaru, making Orochimaru join Akatsuki after finding him. Even Kakashi Hatake, who is noted to be one of Konoha's top shinobi, opted not to face Nagato alone, and ultimately was defeated by the latter alongside Chōza and Chōji Akimichi. Zetsu expressed shock when Nagato was defeated by Naruto Uzumaki, stating that he never thought Nagato would ever lose, even in a weakened state.

After being reincarnated by Kabuto Yakushi and regaining most of his vitality, Nagato was able to easily overwhelm both Naruto Uzumaki in his Nine-Tails Chakra Mode and Killer B whom used the power of Gyūki as well, and Nagato would have killed them both had it not been for Itachi Uchiha's intervention. It took the combined efforts of those three men to successfully defeat him. In this regard, he was considered to be Kabuto Yakushi's second strongest reincarnated shinobi, since the latter noted that he'd have to bring out his trump card after Nagato was sealed.

Nagato's legs were greatly damaged in his battle against Hanzō. As a result, even though he was able to stand on his own, he lacked full mobility. To make up for this, while alive, Nagato used the Six Paths of Pain to fight for him while he remained in a mechanical walker. When he was reincarnated by Kabuto, he used various summons to move around and to keep himself out of range of his opponents' attacks. Though even after being rejuvenated by Gyūki's chakra, which he had absorbed from Killer B, Nagato's mobility was still limited.

Stamina and Life Force
As a member of the Uzumaki clan, he also possessed an exceptionally strong life force and the potential for an incredibly long life span. It has been noted at several points in time that Nagato possessed an unusually large amount of exceptionally strong chakra. Tsunade's Anbu escorts expressed shock on how much chakra he could produce through Deva Path. It was to the point that even after he wiped out Konoha and battled Naruto Uzumaki, he still had enough strength to revive all of the people he had killed since arriving in the village. Likewise, Nagato demonstrated considerable control over his chakra, able to constantly alter its nature to prevent sensors from detecting his signature.

Taijutsu
While not shown in full, Nagato had shown a high level of taijutsu through his Six Paths of Pain, and especially the Asura Path. He was easily able to overwhelm characters as skilled in taijutsu as Kakashi Hatake through his Deva Path with a chakra receiver despite his Sharingan being active. He was also able to contend with Jiraiya's Sage Mode strength, able to block one of his kicks through Human Path with one hand despite the path being blinded. Even the likes of Killer B have been easily restrained by him with one hand. Not only that, when his Deva Path was under a cool down after using the gigantic version of Shinra Tensei he was able to fight Naruto Uzumaki nigh-evenly in taijutsu while he was getting ready to get back into Sage Mode despite Naruto's extensive taijutsu training with the toads.

He has also displayed highly impressive speed and reflexes as well. When rescuing Konan from Hanzō he could cover a massive amount of distance in an instant with Hanzō being unable to react until after he had saved Konan. He could easily react to Naruto's thrown Wind Release: Rasenshuriken, either dodging with less than a second to spare or blocking it with Preta Path, a feat that's only been replicated by the Third Raikage. After his reincarnation, he was able to attack Killer B from behind after blowing him a considerable distance with a focused Shinra Tensei, practically appearing right behind him out of nowhere despite his limited mobility.

As shown in a few instances, Nagato was also very resilient, being capable of withstanding a direct Version 2 Lightning Release: Lariat performed by Killer B without significant injury. He also had a high tolerance to pain, not showing significant discomfort at having both of his legs partially blown apart and incinerated, an injury that would inhibit his mobility for the rest of his life.

Ninjutsu
While acting through the Deva Path, Nagato displayed a wide range of techniques. Nagato was responsible for Akatsuki's meetings by using a technique that allowed him to pick up their thought waves and broadcast them in the form of an astral projection to a specific location. During the time when a tailed beast was being extracted from its jinchūriki, Nagato would set up various ways to stall and prevent potential rescuers from getting to them in time to stop the extraction. Among these various techniques was the Five-Seal Barrier, which prevented anyone from destroying anything that was within its boundaries without simultaneously removing the five seals — an effective method to split enemy forces. Nagato also added another safety procedure, which activated once the seals had been removed, creating copies that perfectly resembled the ones who removed the seals, imitating their battle skills as well. Another technique that Nagato used to delay and stop pursuers from interrupting the extraction was the Shapeshifting Technique, which allowed Nagato to allocate a portion of an individual's chakra and transfer it into a living human sacrifice, allowing the original to fight by controlling their "copy". This allowed the sacrifices to attain whatever kekkei genkai, techniques and weapons the individual possessed. However, once the allocated chakra was finished along with the sacrifice's own, the technique would cancel and the copy would be killed. Nagato was also adept at the use of genjutsu, having used it to install mental barriers and traps in his minions' minds to prevent others from accessing secret information.

Nagato was able to use the Summoning Technique to summon Konan and the other Six Paths. He could also use the Amplification Summoning Technique, which allowed him to summon an animal with a specific condition. Furthermore, when guarding Amegakure Nagato was able to use the Rain Tiger at Will Technique to make it rain. This rain was infused with his chakra and as such, served as a large-scale sensory technique for him in his village. Nagato was also a skilled sensor, being capable of detecting the build up of Amaterasu before it was launched and even pinpoint Kabuto Yakushi kilometres away despite the latter having erected a barrier around his location. He was also able to sense for Fukasaku by placing his hand on the surface of the water Fukasaku escaped into.

Rinnegan
Nagato wielded the power of the legendary Rinnegan, a dōjutsu which was not seen by the world since possessed by the Sage of the Six Paths, the world's first shinobi, and the founder of modern ninjutsu. While not an original wielder, as Madara Uchiha implanted his own Rinnegan into Nagato, Nagato proved able to wield both eyes without drawbacks even in his emaciated state due to his Uzumaki lineage; unlike Obito Uchiha, who could only bear one eye despite his various augmentations and advanced knowledge of the dōjutsu. Even as a child, Jiraiya noted that Nagato had mastered every ninjutsu he taught him and with the Rinnegan, he was able to master all five basic nature transformations as a child — something that was completely unprecedented. His Rinnegan also made him immune to visual genjutsu, as well as nearly invincible in ninjutsu and enhanced his taijutsu. According to Ibiki, the Rinnegan gave Nagato the capacity to use any technique. Similar to the other great dōjutsu, the Rinnegan bestowed him with enhanced vision, allowing him to see chakra and otherwise invisible barrier techniques, which he used during his invasion of Konoha to detect the barrier around the perimeter of the location. Due to his possession of Madara Uchiha's Rinnegan and his own Senju lineage, Nagato was also able to summon and control the Demonic Statue of the Outer Path. Like other users of the Rinnegan, and through the use of the Outer Path, Nagato has shown capable of manifesting chakra receivers. This is an ability that could even be channelled through his Deva Path.

As stated by Konan, Nagato was able to use all of the abilities of the Six Paths Technique himself, as they are all abilities of the Rinnegan. This was later demonstrated after he was reincarnated by Kabuto Yakushi. With his ability to simultaneously utilise the various abilities of the Six Paths Technique with one body, Nagato proved to be a formidable opponent, easily overwhelming Naruto and Killer B at the same time. Naruto noted that since he was using his real body, the strength and speed of his techniques were on a much higher level. However, when fighting on his own, Nagato was without the protection and shared vision offered by the Six Paths of Pain.

Six Paths of Pain
Nagato's most powerful and most used technique was the. This technique allowed Nagato to control six separate bodies as though they were his own. Each of these bodies were reanimated corpses that were both kept mobile by and made use of Nagato's own chakra. By using these six bodies for combat rather than himself, Nagato avoided the risk of being killed in battle by a stronger opponent and compensated for his lack of mobility. As Nagato's vision was linked with the bodies, he essentially had six fields of vision, making it virtually impossible for his enemies to attack any of the bodies without being seen. Nagato's vision was also linked with the King of Hell and the various creatures he summoned, which also possessed Rinnegan. While controlling the Six Paths under the alias of "Pain", Nagato still regarded the bodies as separate entities from himself. The Paths were unable to feel physical pain, as they were merely manipulated corpses, which Ibiki Morino discovered when he tried torturing the second Animal Path.

While making use of the technique, Nagato remained in a machine that moved with six relatively small mechanical legs and used several large chakra rods on his back to transmit chakra to the corpses. From his location, the chakra was picked up by the numerous receivers, modelled as body piercings on each body. To control them, Nagato had to be close by, and ideally at the highest possible point, so he could have the best possible range. Certain techniques, such as Chibaku Tensei could only be used through the Six Paths while they were within a certain range of Nagato. His technique output was also increased while focusing on only one of the Six Paths, although this would leave the others vulnerable and, in the case of overusing the Deva Path's ability, shorten Nagato's lifespan and require the Deva Path's power to recharge for a longer amount of time than usual. Nagato was also able to fire chakra receivers from his mechanical walker and, from a close enough range, control the bodies of those pierced by them with his chakra, although this effect could be resisted.

Based on the six Buddhist Realms of Reincarnation, each body was named after one of the Six Paths techniques: Deva, Asura, Human, Animal, Preta, and Naraka. The only common feature shared by these bodies was their bright orange hair and their Rinnegan. Each also had a vast number of body and facial piercings of various shapes, sizes, and patterns. Each body seemed to serve a specific purpose in battle, such as summoning, repairing, and defensive capability. Nagato himself was regarded as the seventh Pain, the "Outer Path", with control over the forces of life and death. The Outer Path abilities also allowed for Nagato's use of the Six Paths of Pain. Fukasaku stated that the best way of fighting Pain was to take out the Six Paths one at a time, as they were most formidable when fighting together.

Intelligence
Nagato has shown a quite analytical and strategic mind, and could be considered a genius. At ten years-old, he managed to master all five basic Nature Transformations as well as Yin Release, Yang Release, and Yin–Yang Release, which according to Jiraiya is completely unprecedented. When in battle, he was careful to keep his Six Paths of Pain a complete secret, using one or at most three bodies to engage an opponent while keeping the other three in reserve. If the three were defeated, he could easily send the other three to reinforce them and attack the enemy when they are off guard.

When he launched his invasion on Konohagakure, he split and designated his bodies into specific tasks: Asura Path, Animal Path, and Preta Path ran diversionary tactics while Deva Path, Human Path, and Naraka Path ran reconnaissance. With this he was able to engage the entire village at once while keeping his true intentions a secret and ultimately he was able to accomplish his objective in locating Naruto. Due to Konoha starting to figure out his secrets, as well as Tsunade's defiance, he destroyed the village to preserve the former.

When engaging Naruto, he chose a specific formation that would buy enough time for Deva Path's powers to regenerate and keep Naraka Path safe. Using this strategy, he was able to temporarily defeat Naruto despite being exhausted and at a disadvantage from the start. In the anime, similar to his modifying of corpses for the Six Paths of Pain, Nagato has also shown advanced skill in mechanical engineering, able to reprogram and improve a sophisticated robot.

Sasuke Retrieval Arc
Pain made a silhouette appearance with the other Akatsuki members while they were discussing Orochimaru and the Nine-Tails.

Part II
Pain appears frequently as a hologram during the early arcs of Part II, convening the Akatsuki members whenever a tailed beast needs to be sealed. As Part II progresses, portions of his face are shown before culminating in his full début alongside Konan.

Kazekage Rescue Arc
After Gaara was captured by Deidara and brought back to one of their secret hideouts, Pain assembled the other members of the Akatsuki where they extracted and sealed the One-Tail.

Hidan and Kakuzu Arc
After Yugito Nii was captured by Hidan and Kakuzu, Pain led the members of Akatsuki in sealing the Three-Tails and extracting the Two-Tails. He also revealed to Hidan the true motives of Akatsuki after Hidan's two-year membership.

Itachi Pursuit Arc
Jiraiya, Nagato's former master, enters the village through a frog. The moment Jiraiya fully releases himself from the frog, Pain feels a disturbance in the rain. Pain orders Konan to search for the intruder, and stops the rain. As Konan transforms into many pieces of paper, and folds herself into butterfly-like figures, Pain switches from the Deva Path to the Animal Path. Once the process was complete, he departed to search for Jiraiya as well.

Jiraiya, now hidden inside of a body, heads more into Amegakure, and Konan catches him. Jiraiya comes out of the body, and begins to battle Konan. Konan ends up being covered in oil; unable to battle. Pain comes to Konan's rescue and cleans off the oil with foam with his Summoning Technique. Pain then summons a chameleon, and camouflages himself. Jiraiya sets off the Barrier: Canopy Method Formation, after summoning the "clumsy" toad: Gamaken. Pain summons again, but this time, a multi-headed dog. Jiraiya has a very hard time fighting these as it would escape most of Gamaken's attacks, and somewhat regenerate. Jiraiya finishes off the dogs by trapping them in a toad's stomach and digesting them. Pain then summons a drill-beaked bird. The bird follows Jiraiya and makes many attempts to kill him, though fails and ends up getting burned. Pain then summons a rhino, though it quickly gets finished off by Gamaken. Pain then summons a giant ox, and manages to hit Jiraiya. The shield set off by Jiraiya self-destructs, sending the ox flying. Soon after defeating the ox, he completes his Sage Mode activation and summons Fukasaku and Shima. They both easily dispose of the chameleon, revealing the Animal Path. The Preta Path and the Human Path are both summoned, in order to face Jiraiya.

The Human Path attempts to kill Jiraiya, though it gets blinded by Jiraiya's kick to its head. Jiraiya then attempts to burn all three Paths with Sage Art: Goemon, though it gets absorbed by the Preta Path. Jiraiya then uses Ultra-Big Ball Rasengan, though it also gets absorbed. The Human Path attacks once again, and blinded, blocks Jiraiya's punch. The Animal Path gets distracted by a toad, and gets attacked by Jiraiya's Sage Art: Hair Needle Senbon. The Animal Path blocks the attack by summoning a giant panda. Jiraiya analyses their attacks, and escapes into the pipes. While in the pipes, he concludes that genjutsu will give him an opening against the Rinnegan.

The Paths then followed Jiraiya, and while doing so, get caught in genjutsu. Jiraiya then destroys the Paths. As Jiraiya leaves, he lets his guard down. One of the Paths manages to sneak up behind him, and removes his arm. The other Paths come together, including the ones that got killed (which were rejuvenated by the Naraka Path). Jiraiya manages to kill the Animal Path, though ends up being brutally killed in turn. As Jiraiya sinks into the deep depths of the sea, Pain holds a moment of silence in respect for his former master.

Tsuchigumo Kinjutsu Arc
In the anime, after getting a replacement for the Animal Path, Pain is shown to have been assigned to capture the Six-Tails, which was sealed within Utakata, a missing-nin from Kirigakure. During his search, the Animal Path had his Giant Multi-Headed Dog scout the area, where it found and killed a group of Kirigakure hunter-nin led by Tsurugi. When Utakata later sought out Tsurugi and his men to turn himself in, he instead found Pain; Pain told Utakata that he would be needed to create his world, and informed the jinchūriki that he would be taking the Six-Tails. The Six Paths of Pain quickly captured him and then later extracted the beast.

Invasion of Pain Arc
With only the Nine-Tails and Eight-Tails remaining, Pain and Konan set out for Konoha after receiving orders from Tobi to capture the former. Eliminating the border guards upon their arrival, they infiltrated the village and dispersed, with each of the six Paths having a specific task: the Asura, Preta, and Animal Paths served as diversions, while the Deva, Human, and Naraka Paths and Konan in charge of reconnaissance. While exploring and laying waste to the village and its inhabitants, the Deva Path was confronted by Kakashi Hatake. The Asura Path came to its aid and together they overwhelmed Kakashi and his allies, but the Asura Path was destroyed.

Across the village, the remaining Paths continued their tasks, fighting whatever Konoha ninja they came across. The Deva Path met with Tsunade, the Fifth Hokage, who refused to reveal Naruto's location. Elsewhere, the Human Path used its unique interrogation technique on Shizune to learn that Naruto was at Mount Myōboku. Declaring that he would teach Tsunade the pain that Konoha had been so ignorant of, Nagato had the Deva Path use Shinra Tensei to obliterate the village while Konan and the other Paths withdrew.

As the smoke cleared, the Deva Path found that Naruto had returned with his toad allies. In retaliation for the village's destruction, Naruto swiftly crushed the newly-restored Asura Path and began his fight with the remaining Paths of Pain. The Animal Path called upon its summons to attack Naruto, who parried them with the aid of his toads and proceeded to defeat the Preta Path. Soon afterwards, Naruto eliminated the Human Path with his Wind Release: Rasenshuriken, and then teamed up with Gamabunta to defeat the Animal Path.

With four of the Paths gone, the temporarily powerless Deva Path protected the Naraka Path, which restored the Preta Path. The Preta Path absorbed a second Rasenshuriken, but it had only been a diversion to give Naruto an opportunity to finish off the Naraka Path. The Deva Path, its power returned, detained Naruto so that the Preta Path could capture him and absorbed his chakra to immobilise him. Doing so caused it to absorb senjutsu chakra, which had the side effect of turning it to stone. Naruto escaped its clutches, but was seized once again by the Deva Path, who pinned him to the ground with chakra disruption blades. The Deva Path lectured Naruto about the chain of hatred, pain, suffering, and war that the ninja system brought to the world, and how he planned to use the tailed beasts' power to achieve peace and end conflict. He asks if Naruto can think of a better solution, but Naruto does not respond.

Before the Deva Path could take Naruto away, Hinata Hyūga came to his defence. When she is apparently killed, Naruto became enraged and entered his six-tailed form, with which the Deva Path could not compete in its current condition. The Deva Path retreated to a location closer to Nagato, who had secluded himself nearby in order to control the Six Paths of Pain. This allowed the Deva Path to use Chibaku Tensei, trapping Naruto in a massive orb of earth and debris. This victory was short-lived, as Naruto soon progressed to an eight-tailed form and broke free of the Chibaku Tensei. Realising that he would have to make the sphere larger, it suddenly began to crumble and Naruto, reverting to his normal form, emerged from the ruins.

Reflecting on the earlier lecture, Naruto demanded an opportunity to speak with Nagato, but was denied and attacked by the Deva Path. After failing to use Wind Release: Rasenshuriken twice, by taking advantage of the five second gap between the Deva Path's ability, Naruto was able to defeat it with a well-timed Rasengan. He removed one of its chakra receivers and inserted it into his skin to track the signal back to Nagato. Naruto goes to see him, but when he arrives Nagato fires another chakra receiver at him to try and control him. Naruto resists it despite his close proximity to Nagato. Although angry with Nagato for killing Jiraiya and destroying Konoha, Naruto asks how, as a fellow student of Jiraiya, he could have strayed so far from their master's teachings. Hoping that Naruto would come to agree with his solution for peace, Nagato told him his past, of his two great sorrows and how he came to believe pain would save the world.

Although Naruto agreed with Nagato's ultimate conclusion, he rejected it for differing with Jiraiya's ideals. In doing so, he answered Nagato's earlier question about how to attain peace: by "breaking the cycle of hatred". He decided not to attempt to kill Nagato, as that would only perpetuate the cycle of revenge.

Amazed by Naruto's resolve and remembering Jiraiya's teachings, Nagato decided to put his faith in Naruto's answer and used the Outer Path — Samsara of Heavenly Life Technique to revive all the Konohagakure citizens killed during his invasion at the cost of his life, causing his red-hair to turn pure white due to the overexertion. With his final breath, dying with a smile on his face, Nagato wished for Naruto's dream of peace to come true and, in regard to both the youth and their mentor's book, felt it was like "the work of a true god".

Chikara Arc
In the anime, Nagato is summoned by Kabuto to battle Team Kakashi, who are investigating the massacre that he brought about in The Hole. Quickly after being summoned, Nagato's coffin vanishes with Kabuto questioning if the Impure World Reincarnation is incomplete.

Confining the Jinchūriki Arc
In an attempt to both impede Tobi and coerce him into joining forces during their initial encounter, Kabuto Yakushi demonstrated his capabilities by reincarnating many of the deceased members of Akatsuki, including Nagato, using Summoning: Impure World Reincarnation. Despite appearing almost exactly in the same condition as the time of his death — visibly emaciated and with white hair — he lacked the chakra transmitters that were formerly embedded into his back.

Shinobi World War Arc
Mobilised alongside Itachi as the Fourth Shinobi World War against the Allied Shinobi Forces commenced, Nagato though reincarnated was still unable to fully use his feet and as such was initially carried upon Kakuzu's back. Later supported by Itachi, the now-isolated pair walked throughout the night, conversing about Akatsuki and how they both were and continued to be used simply because of their powerful dōjutsu. After pausing at a shrine and discussing Kabuto's influence on Tobi's plan, they march onwards till dawn, when they encountered Naruto and Killer B. Detecting their presence, Nagato noted a nostalgic feeling, before lamenting having to fight Naruto again.

Pleased to see him nonetheless, he congratulated his fellow disciple on gaining control of the Nine-Tailed Demon Fox and overcoming his hatred. As they attacked involuntarily, Nagato warned them of Itachi's impending assault, before being shocked at the revelation of the truth behind the Uchiha clan massacre. Using Banshō Ten'in to draw both Naruto and a huge rock towards one another, he marvelled at Naruto being able to deflect the attack. Remarking that the distance between them was good as he had limited mobility, Nagato jokingly retracts this, after summoning his dog and bird. As they clashed, Nagato told Naruto to attack him instead of the summons, because the dog would just continually multiply when struck.

After a crow emerged from Naruto's mouth and sensing a change in Itachi, Nagato warned Naruto that the latter was about to use Amaterasu. However, when his summon is attacked instead, Nagato discerned the crow's purpose but only after he himself was engulfed in black flames. Falling to the ground, he began to burn before later repelling the flames with Shinra Tensei.

With Kabuto erasing his consciousness, now regenerated and concealed within his summoned chameleon's mouth, Nagato unleashed a large-scale Shinra Tensei on his opponents. Aiming to attack B amidst the devastation, he is instead struck by the former's Version 2 Lightning Release: Lariat, but avoids any significant injury by absorbing B's chakra. This chakra revitalised Nagato's body, returning him to his state prior to being emaciated by the Demonic Statue of the Outer Path. Casting B aside and whilst Naruto was restrained by the still invisible chameleon, he attempted to remove the latter's soul.

After Kabuto decided to confine the jinchūriki's bodies and souls separately within the King of Hell, Nagato halted B's attempt to save Naruto, using two additional arms grown from his shoulder. With the two restrained, he started charging a powerful blast, only to be separated from them through Itachi's intervention. Nagato then proceeded to use Chibaku Tensei but even this was stopped, when its central sphere was destroyed by the combined effort of their strongest long-range techniques. Impaled by Susanoo's Sword of Totsuka before the dust settled, Nagato apologised to Itachi as his consciousness returned. Taking this opportunity to impart his last words, he told Naruto that he was part of a trilogy that included Jiraiya — who was perfect, himself — whom he deemed a failed work, even his master can't acknowledge him, and finally Naruto — whom he asked to create a masterpiece so as to erase his wrongs. Bidding them farewell as the sword seals him, Nagato remarked that he was going to rejoin his teacher in the afterlife. With Nagato sealed, Kabuto cursed the fact that Nagato's mobility was hampered and decided to resort to his "reserve".

Legacy
With Nagato's death, Konan defected from the Akatsuki as she stated that she no longer had a reason to remain since both Nagato and Yahiko were dead. She took Nagato's body, and that of Yahiko's back to Amegakure with her for burial. Both of their bodies were dressed in Akatsuki mantles, and laid in a large body of flowers within a shrine. Because Nagato gave his life to help Naruto achieve peace, Konan vows Amegakure's allegiance to him in this pursuit. It was also due to this battle that Naruto noted that he knew what true loss was, and from the subsequent meeting with Nagato and Konan that spurred Naruto on to find peace in the world.

Tobi was surprised by news of Nagato's death and, more so, his "betrayal", having wanted Nagato to save the Samsara of Heavenly Life Technique for Madara. He later confronted Naruto about this to found how he could have swayed Nagato. Naruto asserts that Nagato truly did aspire to bringing peace unlike Tobi, who is solely obsessed with power, despite his ambition being the same as Nagato's.

Soon after, Tobi arrives to Amegakure and kills Konan to get the location of the shrine where Nagato is laid to rest. Stating that he was the, Tobi takes Nagato's body into the other dimension. Soon after, Tobi replaces the left Sharingan he lost from fighting Konan with one of Nagato's Rinnegan eyes. Later, during the Fourth Shinobi World War, Tobi duplicates Nagato's Six Paths of Pain method on the reincarnated Yugito, Yagura, Rōshi, Han, Utakata, and Fū as his Six Paths of Pain. Nagato himself viewed the legacy he left behind as a poor one and hoped that Naruto, his fellow disciple would leave a better one that would erase his own.

His sensory skills were such that he told Itachi where their summoner was. The deceased Uchiha would use this information to find Kabuto and force him to release the technique, thus helping the Allied Shinobi Forces during the war.

Video Games
Nagato himself is only playable in Naruto Shippūden: Ultimate Ninja Storm 3, as he appeared upon being reincarnated by Kabuto during the Fourth Shinobi World War in his youthful form after absorbing some of Gyūki's chakra. In all other instances, it is Pain who is playable. The player generally controls the Deva Path, with the remaining paths all playing roles in his attacks in the Storm series. The Asura Path and first Animal Path are also playable in Naruto Shippūden: Ultimate Ninja Heroes 3.

Creation and Conception
In Naruto Hiden: Sha no Sho Character Official Data Book, Kishimoto briefly explained the philosophy behind Pain's design, stating, "He's Akatsuki's leader, so he has to look fairly cool, but I still wanted him to look dangerous. Since his name is 'Pain', I decided to add some piercings to his body, like he's the kind of guy who would inflict pain upon himself". Notable among the few unused concept designs is a small sketch in which he appears to wear a partial face mask and feather, or horn-like accessories fitted to his forehead protector.

When first appearing in the anime, Pain's eyes were depicted with an incorrect colour scheme where the two centre rings of the Rinnegan were coloured separate shades of grey, while the outermost ring was flesh-coloured, and the ring in between was white. Following his appearance in chapter 377 of the manga, which featured the first official colour illustration of his face, the colour scheme was corrected.

Several of Nagato's abilities were inspired by Buddhist beliefs and terminology, and he thought that enlightenment was reached through experiencing and understanding pain and suffering, similar to a path the Buddha took but then later rejected.

Trivia

 * Nagato is an ancient Japanese name, as well as a World War II era battleship.
 * Nagato's name means "long-lasting gate".
 * The original Six Paths of Pain were composed of individuals whom Jiraiya met during his search to find the "Child of Prophecy".
 * As the creatures Nagato summoned with the Animal Path were pierced with chakra receivers, much like his Six Paths of Pain, it could be assumed that they were also being controlled. Nagato was also able to see through their eyes.
 * When he was young, Orochimaru offered to kill Nagato and his friends so they would not have to suffer the horrors of war (at least any more than they already had), but many years later he let Orochimaru join Akatsuki. It is unknown if Orochimaru is aware that two of the three orphans he proposed to kill became his superiors.
 * Jiraiya stated that because Nagato manifested the Rinnegan he believed him to be the reincarnation of the Sage of the Six Paths himself. This would later be proven false when it was revealed that the Rinnegan was surgically implanted into his sockets by Madara, instead of them being a natural manifestation.
 * In keeping with his "God" theme, his theme-song is "Girei" — a haunting theme that consists of holy chanting.
 * Nagato may be named after the famous ninja Fujibayashi Nagato who, in the 16th century was considered to be one of three greatest Iga jōnin. The other two being Hattori Hanzō (Hanzō's supposed namesake) and Momochi Sandayū (Zabuza Momochi's supposed namesake).
 * Studio Pierrot's Settei sheets of Nagato show that he was 149 cm when he first met Jiraiya, and 163 cm when Jiraiya left Amegakure.
 * According to the databook(s):
 * His hobby was practising ninjutsu.
 * His desired opponent was anyone in order to protect his friends.
 * His favourite food was grilled fish and stew.
 * Nagato's favourite phrase was . As a child, it was "Growing up".
 * As Pain, he wished to fight Naruto Uzumaki (or more specifically the Nine-Tailed Demon Fox).

Quotes

 * (To Jiraiya) "Peace… I don't know how to get there… but… but someday I'll break the curse. If there's such a thing as peace, I will find it!"
 * (To Hanzō, through the Deva Path, before killing him) "Have you forgotten my face? Danzō, who we had allied with, had betrayed us. You, who completely focused on your own protection, are trash. There was a time when I respected you. But now, you've changed. And you can't even figure out why you've lost to me… Vanish, Hanzō."
 * (To the Deva Path) "You will always be the leader of Akatsuki… Yahiko."
 * (To Akatsuki) "We're both of the same breed, after all… motives for war are of no concern. Religion, ideology, resources, land, grudges, love, or just because… No matter how pathetic the reason, it's enough to start a war. War will never cease to exist… Reasons can be thought up after the fact. Human nature pursues strife."
 * (To Jiraiya) "Even a foolish child can grow up in a right way, when he learns what pain is. Knowing pain controls ones thoughts and decisions."
 * (To Jiraiya through his Six Paths) "We are Pain! We are God!"
 * (To Utakata) "I'm going to build a new world."
 * (To Tsunade) "You think you're the only ones who matter. You think you can put off death. But that peace made you foolish and thoughtless. If you kill someone, someone else will kill you… this hatred binds us together. I want you to feel pain, to think about pain, to accept pain, to know pain."
 * (To Naruto) "I see… That is noble of you. That is justice indeed. However… My family… My friends… My village… They suffered the same fate as this village by you ninja of Konoha. How is it fair to allow only you people to preach about peace and justice?"
 * (To Naruto) "''Love breeds sacrifice… which breeds hatred… Then you can know pain.
 * (To Naruto) "We are both but men, driven to seek vengeance under the banner of justice. However… if there is justice in vengeance, then justice will breed only more vengeance… thus forging more links in a chain of hatred."
 * (To Naruto) "If you don't share someone's pain, you can never understand them. But just because you understand them doesn't mean you can come to an agreement. That's the truth."
 * (To Naruto) "You and I are no different. We each act according to our own sense of justice. The justice I have meted out against Konoha is no different than what you are trying to mete out against me."
 * (To Naruto) "You are an odd kid… You remind me of myself when I was young… I couldn't believe in what Jiraiya believed in… nor believe in myself… but you chose a different path. In you I can see another future. I… will believe in you…"
 * (Last words to Naruto before dying) "Dying like trash… never ending hatred… pain that never heals… that is war… Naruto… this… is what you must face… The book… and you… It's like… someone… set this all up… Or… maybe… this… is… the hand of the real God… My role is over now… Naruto… you… can really—"
 * (Last words to Naruto before being sealed)