Background
A student from Class 77-B of Hope's Peak Academy, Nagito is classified as the Ultimate Lucky Student, similar to Makoto Naegi from the first Danganronpa. Like Makoto, he was able to attend the school as the recipient of a lottery despite having no other real Ultimate talent. Unlike Makoto, Nagito had a very traumatic childhood that left him alone and in search of the Ultimate Hope, to the point where he calls himself the "Ultimate Ultimate Fan."
At some point after The Tragedy happened that enveloped the whole world into despair, Nagito joined the Remnants of Despair, a group of students from Hope's Peak Academy who worshipped Junko and were corrupted by her into spreading despair even after her death. Nagito somehow managed to recover the dead Junko's left arm and cut off his own to replace it with hers, thinking that it would be the ultimate triumph of Hope over Despair.
Danganronpa 2: Goodbye Despair
When he is taken along with 14 other students to Jabberwock Island in Danganronpa 2, he hints at his own past in conversations with Hinata Hajime, the main protagonist whose Ultimate talent is unknown at the start. When the Killing Game begins on the island, Nagito tries to use his luck to commit the first murder, thinking it will teach the rest of the Ultimates to work together to find their Hope. However, his luck also indirectly ends up saving him when the first victim pushes him away before he can commit the act, letting someone else kill the first victim instead.
As the game continues, Nagito alternates between trying to find the real killer in each case and trying to help them. When the rest of the class questions his loyalty, Nagito justifies it as whatever outcome ultimately happens is the one that will produce the greatest Hope to overcome any Despair. In the case at the Funhouse, Nagito uses his luck to solve a deadly puzzle and is awarded an old file detailing the profiles of the class as well as details of the previous game. Using the information contained within he tries to expose the identity of the traitor in hopes of ending the game.
After the Funhouse case, Nagito decides to set up a scenario where he blows up part of the island hotel and threatens to blow up the rest of the island unless the traitor reveals themselves. When no traitor steps forward, he sets up an elaborate murder scene by filling a fire grenade canister with a deadly poison gas and tricking the group into setting a warehouse on fire, where he has already almost killed himself with several wounds.
During the trial, it's revealed that Nagito set up the scene hoping his Ultimate Luck would lead the traitor to grab the poisoned canister and deliver the killing blow without realizing it. He also tried to set it up so that his death would be ruled a suicide instead of a murder, and that by picking Nagito himself as the culprit, the traitor would win the game. Instead, the surviving classmates choose the real traitor as the murderer, ruining his plan but ultimately allowing the game to end.
In the epilogue, it's hinted that Nagito is still alive but comatose, like the others who were "killed" in the game, while the survivors are looking for a way to bring them back to consciousness.
Danganronpa Another Episode: Ultra Despair Girls
In this game, he is referred to as Servant, claiming that he was about to be killed by the Warriors of Hope but they spared him after he begged for his life and offered to be their slave. Despite his meek demeanor on the outside, he secretly helps Komaru Naegi from behind the scenes, feeding her extra ammo for her weapon and occasionally sabotaging the efforts of the murderous children before they can complete their master plan.
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