Nagato, also known by the alias Pain, is introduced in the Itachi Shinden novels and their anime adaptation as a significant figure whose ideology and actions parallel and contrast with those of Itachi Uchiha. His background is rooted in the war-torn country of Amegakure, the Village Hidden in Rain, where he was born as a descendant of the Uzumaki clan. As a young child, his parents were killed by Konoha shinobi during the Second Shinobi World War, an event that first awakened the Rinnegan in him, a powerful dojutsu that had been transplanted into him by Madara Uchiha without his knowledge. After becoming an orphan, he was found and cared for by two other war orphans, Yahiko and Konan, and the three formed a deep bond, dreaming of creating a peaceful world free from the endless cycle of conflict. They later sought training from the legendary Sannin Jiraiya, who, upon witnessing Nagato's Rinnegan, believed him to be the prophesied child who would bring about a revolutionary change in the world and taught them ninjutsu for three years.

Nagato's personality in his youth was idealistic and gentle, shaped by Jiraiya's teachings and his camaraderie with Yahiko and Konan. He was initially hesitant to use violence and shared his friends' hope for a peaceful resolution to the world's wars. However, the trauma of losing his parents, compounded by the later betrayal and death of Yahiko at the hands of Hanzo, the leader of Amegakure, and Danzo Shimura's Root organization, fundamentally transformed him. The overwhelming grief and sense of betrayal caused his personality to harden into a cold, detached pragmatism. Adopting the name Pain, he came to believe that true peace could never be achieved through understanding and compromise, but only by forcing the entire world to experience the same unbearable suffering he had endured. This philosophy held that shared pain would create a deterrent against war, as no nation would risk the mutual destruction that would follow.

His motivations were driven entirely by this radical ideology. He sought to gather all nine tailed beasts and use their combined power to create a superweapon capable of instantaneous, massive destruction. By threatening the entire world with this ultimate weapon, he aimed to force all nations into a forced truce, a state of peace maintained by the fear of annihilation. This goal made him the figurehead leader of the Akatsuki organization, which he redirected from Yahiko's original vision of peaceful negotiation toward a campaign of terror and conquest.

In the Itachi Shinden story, Nagato's role is that of a philosophical foil and a looming presence within the Akatsuki. His interactions with Itachi are not extensive in terms of direct dialogue, but the narrative draws clear parallels between their two paths. Both were child prodigies who witnessed the horrors of war at a young age and sought peace. However, while Itachi chose to sacrifice his own clan and reputation from within the system to protect Konoha, Nagato chose to challenge the entire system from the outside, embracing the role of a godlike antagonist to force change on a global scale. The Itachi Shinden novels explore this contrast, showing how similar beginnings can lead to radically different conclusions based on the choices made in response to trauma.

Key relationships in his life include his bond with Konan, who remained his most loyal follower and partner throughout his transformation, and his complex connection with his fallen friend Yahiko, whose body he repurposed as the Deva Path of Pain, the primary body through which he led the Akatsuki. His relationship with his former master Jiraiya is also central, as their eventual confrontation and Jiraiya's death at Nagato's hands underscores the tragic divergence of their philosophies. Additionally, Obito Uchiha, manipulating events while disguised as Madara, secretly guided Nagato's path, ensuring that his Rinnegan would be used to further Obito's own plans.

His development throughout the narrative traces a tragic arc from an innocent, hopeful child to a hardened, messianic figure who believes himself to be a god of retribution. The novels delve into his internal conflict, showing that beneath the cold exterior of Pain, the original Nagato still lingered, burdened by the memory of his friends and the teachings of Jiraiya. This internal struggle eventually leads to his confrontation with Naruto Uzumaki, which is portrayed in the main Naruto series but is thematically prepared by the character study in Itachi Shinden.

Nagato's notable abilities stem entirely from the Rinnegan, which grants him mastery over all six types of chakra nature transformation and access to a suite of techniques known as the Six Paths of Pain. He controlled six individual corpses, each assigned a specific path with unique powers. The Deva Path, using Yahiko's body, could manipulate attractive and repulsive forces with techniques like Shinra Tensei and Bansho Ten'in, as well as the ultimate planetary devastation technique Chibaku Tensei. The Asura Path could mechanize his body with weapons and extra limbs. The Animal Path specialized in summoning a variety of creatures. The Human Path could extract souls by touch. The Preta Path could absorb chakra and ninjutsu. The Naraka Path could summon a king of hell capable of restoring other paths or extracting information. These six bodies operated with shared vision, making them an extremely coordinated and versatile fighting force. Nagato himself, physically frail and immobile due to his extensive use of these techniques, controlled them from a hidden location, projecting his will through chakra receivers piercing the bodies.