"Love breeds sacrifice… which breeds hatred… Then you can know pain."
Nagato lived with his parents in a village somewhere on the outskirts of Amegakure, the Village Hidden in the Rain, due to the never ending rain that fell on the country. 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 parent death, Nagato in his grief used the Rinnegan for the first time and killed the assailants. Thus orphaned by the conflict, Nagato banded together Konan who found him on the streets and Yahiko, who already lived with the little girl. The three children lived alone for a while until they stumbled on a fight between three ninjas of Konoha and Hanzo of the Salamander, the leader of Ame. The kids were caught in an explosion and the stray dog Nagato has adopted, Chibi, died.
They found the three Konoha ninjas some time later and managed to convince one to stay to teach them the ninja way. Jiraiya was his name and his kind heart refused to see three young orphans alone: he vowed to teach them how to defend themselves before returning to Konoha. And thus the three of them began to live together: with a Ninja to provide them with food, shelter and protection the Ame orphans were free to concentrate on their training.
Jiraiya stayed three years and then returned to his village: he had taught them all he could and encouraged them to seek peace, especially Nagato whom he believed to be the 'Child of the Prophecy', the one who could bring peace to the entire ninja world. The three friends were first devastated by the departure of their beloved sensei and father figure, but soon continued to train on their own, the three of them wanting to get in order to realize their and their Sensei's dream: bring peace, to Ame first and maybe to the world as well!
Once adult, they formed an organization that promoted negotiations rather than fights, a first in the Ninja world: they were often called to resolve matter without violence or drive out rogue ninjas and bandits without killing. Their little group soon grew stronger and new members joined. Yahiko, their leader, named it 'Akatsuki', as it was the dawn of new era of peace.
But Hanzo the Salamander became wary of this new force in his country, and his paranoia, helped by the whispers of Danzo, an extremist from Konoha who didn't like the Akatsuki's speech of peace, reached the point he decided to eliminate the 'threat'. Under the pretense of meeting them to discuss peace, Hanzo kidnapped Konan and gave this ultimatum: if he wanted her to stay alive, then Nagato had to kill Yahiko with his own hands. Rather than forcing his friend to make such a choice, Yahiko impaled himself on Nagato's kunai. Traumatized by the suicide of his almost-brother, Nagato activated the Rinnegan and summoned an enormous statue, the Gedo Mazo which devoured the souls of all the Ame Ninjas loyal to Hanzo present on the scene, the Salamander himself barely escaping with his life. Alas, during the fight, Nagato's legs were caught in an explosion and the burns were severe: worse, the summoning of the Gedo Mazo Statue left him dangerously emaciated and with strange black rods planted into his back.
The aftermath of this catastrophe left both Nagato and Konan vulnerable mentally and a man who called himself 'Madara', like one of the most famous and most dangerous ninja to have ever existed, jumped on the occasion. Madara manipulated Nagato to believe that only bringing pain and fear to the different countries could bring peace to the entire world: the strange man affirmed that people could only grow if they knew pain, and Nagato believed him. But the Rinnegan user was now crippled, unable to walk by himself, let alone fight. To solve this matter, Nagato implanted in Yahiko's corpse black rods similar to the ones now stuck in his back and a copy of his dangerous pupils as well: due to the connection that now linked them through the rods, the red head was able to use the body of his best friend as a puppet while himself stayed in the shadows, renaming himself 'Pain'. Five other corpses joined Yahiko and the Six Paths of Pain were born.
The first action of Pain was to find Hanzo and murder not only him, but his family close or not, his followers and even ninjas from other countries that agreed to his ideals. No one was spared, not even toddlers or pregnant women. Most of the people of the village Hidden in the Rain were relieved to see the tyrant Hanzo gone, and in honor of his feat and his power, named Pain their God and Konan his Angel. Then he reformed Akatsuki with powerful rogue ninjas and began his quest to find the nine Bijuus, monsters made of chakra and now sealed inside human beings. Madara had told him that once extracted from their hosts (killing him in the process.) and contained within the Gedo Mazo Statue, they would form a weapon of unlimited power, capable to bring pain in any point of the world.
At this point, Nagato was mostly gone under his 'Pain' personality, focused on his goal of bringing peace through pain. Convinced that his suffering had allowed him to reach another plan of existence, he told himself that he was indeed a God, even though he was so easily manipulated by Madara. For eight years he captured hosts and extracted their Bijuus, slowly getting closer to his goals.
But resistance began to build: the Nine Tailed Fox, held by a certain Uzumaki Naruto was proving difficult to capture, and many members of Akatsuki had already been cut down. Pain decided to take the matter in his own hand: first he killed his former teacher when Jiraiya went to investigate Ame, without feeling any remorse, and then moved against Naruto's village, Konoha. It was also a way to avenge the murder of his parents by the hands of ninjas from this very village. Using the six Paths as his personal army, he invaded the village, killing many innocents and finally razed most of it in one attack.
Fortunately for Konoha, Naruto came on the scene and fought Pain in an epic fight, destroying five paths and then battling the Deva Path, Yahiko's corpse. Finally managing to defeat this Path as well, Naruto went to meet Nagato in person. Both had the same sensei, and both wanted peace in their own ways: the Host refused Nagato's way because it didn't follow Jiraiya's teaching, and told his fellow disciple that he would reach peace by breaking the circle of hatred. Naruto then refused to kill Nagato for revenge, even though the Rinnegan user had killed many of his friends in his attack.
Amazed by Naruto's resolve and remembering Jiraiya's teachings, Nagato decided to put his faith in Naruto's answer and used a forbidden jutsu to bring all the Konoha villagers he had killed in his attack back to life. The technique was too much for his already weak body, and Nagato passed away with a smile, confident that his fellow disciple would be the Child of the Prophecy and bring peace to his world.
But when he thought everything was finally over, Nagato woke up in a strange land, when your will can bend the world around you. The grief over his actions and the many innocent lives he had taken during his reign as a 'God' had followed him in this city, and he now needs to learn how to live with this weight on his conscience.
When he was young, Nagato was a naive, eager to please little boy. He had suffered the loss of his parents and lived on the streets for a while, but gained new friends and a new family with Konan and Yahiko as his brother and sister, and Jiraiya as his substitute father. Then fate decided to take away his most precious persons: first his dog, then his sensei was gone, his brother died, his sister/maybe-something-more saw her kind heart twisted by his ideals and he killed the one he had loved like a father with his own hands, thinking he was an obstacle on his quest of "peace". It is a tribute of his own strength of character that Nagato didn't simply lost it when Naruto brought him back to his senses.
But due to the senseless beating Life gave him, Nagato is now an embittered man, reluctant to trust. He is wary of everyone, hiding behind a neutral expression and polite words. Between his training as a ninja and the years he spent leading a criminal organization, he became quite good at hiding his feelings and decipher all the political mumbo jumbo he had to go through as the leader of Amegakure.
The trusting nature he had as a child is still somehow present, but Nagato covers it with wariness and keeping others at arm’s reach. The Rinnegan user tries very hard to not get close to anybody, sure that people just want to use him and the power of his eyes. After all, that could have been the story of his life: being used, first by Hanzo, then by "Madara". He knows now more than anyone how to recognize the ones that coat the poison of their words in honey, and even when he is not sure if the person he is speaking wants to manipulating him, Nagato will always assume it is the case.
Since life didn't want to let go of his favorite toy, Nagato is now confronted to the guilt of his acts during his reign as God of Ame and leader of the Akatsuki. He has killed and ordered to kill innocents, razed countries. He resurrected a whole village, but it is nothing but a drop of water in a lake, at least for him. His God complex is now gone, replaced by crushing guilt and inferiority complex: him who was supposed to be the Child of the Prophecy, the one that brings Peace to the world did the exact opposite. What is worse than that? Like a puppet on a string, he and the power granted by his eyes only brought destruction and the war he hates so much to innocents. Death was redemption.
But his kind heart is not totally gone. Nagato has a soft spot for kids, especially orphans as he is one himself and won't lose an occasion to spoil them. Same can be said for the animals, especially if they are small and cute. If you manage, by some miracle, to get pass his walls, you will find a steadfast friend, ready to do anything to protect you and make you happy. Nagato does have a sense of humor, even though it is well hidden under his polite facade. He is also way more carefree and relaxed when surrounded with friends.
The Rinnegan user is also a very respectful man, especially toward the dead and his opponents, proven that they are respectful in return. If it isn't the case, he is just going to Shinra Tensei' their ass to Mars.
Nagato has numerous abilities, given both by his lineage and his eyes: Nautilus has taken them away, but the ninja is working very hard to Bend back. A complete list would be too long to post here, but you can find it here. But for all he is a formidable warrior, and a lethal one, he cannot fight for very long: his legs, crippled when he was younger, refuse to carry him as they should and he has to compensate for them using his Bending, which he cannot do for very long.
Captain Miklo Braca:
One of the first persons Nagato met on Nautilus. Being both soldiers and no quite understanding the general mindset of Nautilus' population, they stick together, even calling each other friends in the secrecy of their thoughts. And since Scott Summer arrived and wormed his way in both of their hearts, they get along even more, mostly because they regularely have to pull him out of trouble.
A young, broken man, pretty much like Nagato himself. Now aware of what destiny lies in front of the teenager, Nagato is doing his best to keep an eye on him and steer him in the right direction, so he wouldn't end up like the ninja.
The… man? skeleton? who took him in when Nagato first arrived. The Ninja deeply respects Death, even though they do not talk that often.
A young fox-boy, still very naive but gifted enough in Bending to teach Nagato, who jokingly calls him 'Sensei'. The ninja's protective instincts are always tingling when near Tails, and he can go papa bear on whoever is hurting him.
It seems that even in Nautilus, Nagato's life is haunted by foxes. Nott is young, though less than Tails, and the ninja comes to him when he needs something explained about Nautilus or the weird ways of its inhabitants.
John, being the 'enemy' of Braca back in their world, has an ambiguous position in Nagato's mind. Not an enemy, but no friend either. Since a Storm when Nagato, transformed in a dog and not in his right mind, showed him his most precious possession, John is under surveillance almost 24/7.