Em Danganronpa, os jogadores mergulham em uma série de julgamentos de classe e expõem as mentiras e contradições de seus colegas de classe para descobrir quem está por trás de cada assassinato terrível. Em cada julgamento, os jogadores devem usar as evidências e testemunhos coletados durante sua investigação para derrubar literalmente as afirmações de seu oponente.

Hope's Peak Academy is a government-funded private high school recognized nationwide as the cradle of hope and prosperity, providing a comprehensive education for "ultimate" students of all stripes. Thanks to a national lottery, one extremely lucky but otherwise ordinary student—Makoto Naegi—has been chosen to attend this prestigious institution. But when Makoto arrives for his first day of class, he suddenly loses consciousness, and when he wakes up, he finds himself in a classroom in the school, with the windows barred and the doors locked. As he explores the abandoned, dirty halls, it becomes clear that something is very wrong. He and his new classmates make their way to the gymnasium, where a demented robotic bear, calling himself Monokuma and claiming to be the school's headmaster, makes a declaration: "You're all going to be living here from now on. If you want to go free, your only choice... is murder. " And so... fifteen high school students gathered from across the country have been imprisoned. Their strength, their commitment, their very humanity will be tested time and time again. Why must they clash in these class trials? Who's the mastermind behind it all? And what is this shadowy figure really after? The battle against the looming, invisible enemy known only as despair is about to begin.