Nagito and his classmates fell victim to Junko's brainwashing, transforming them into the remnants of despair. During the catastrophic events known as the Tragedy, the members of Ultimate Despair unleashed a wave of terror across the globe, spreading hopelessness far and wide. Even after Junko's demise, her followers went to extreme lengths, harvesting parts of her body in a twisted attempt to keep her spirit alive within them. In a shocking act of devotion, Nagito severed his left hand and replaced it with hers. The remnants then concocted a bizarre scheme to implant an AI version of Junko into their bodies, hoping to resurrect their fallen leader.

Nagito embarked on a journey to Towa City, seeking refuge. Unbeknownst to the Warriors of Hope, he was likely one of the Ultimate Despair tasked with overseeing the Captives before their fateful encounter. Initially, the children were oblivious to his true nature and plotted to eliminate him. However, after he desperately begged for his life, they opted to keep him alive as their servant. They adorned him with a collar and chain, referring to him merely as "the Servant," treating him as if he were less than human. His incessant chatter and tendency to misinterpret commands annoyed them, yet he somehow commanded a degree of authority over the Monokuma Kids, able to issue them orders.

In reality, Nagito had orchestrated his own capture to further his own ambitions, aligning himself with Monaca. During this time, he stumbled upon the unconscious Komaru, who had been taken captive. Seizing her Megaphone Hacking Gun, he meticulously analyzed and weakened it to ensure "game balance." After several days, she finally regained consciousness and was greeted by the sight of the Servant. With a smile, he returned her weapon.

"I'll enhance your little gun, but first, the Warriors of Hope want to see you. And a word of caution: keep that weapon concealed if you wish to stay alive."