Danganronpa: The Animation follows the events of those of the video game Danganronpa: Trigger Happy Havoc. The series follows 16 high school students locked inside "Hope's Peak Academy", their High School. The students are threatened by a anthropomorphic bear, known as Monokuma, who gives them only one way to leave the Academy, to murder another student, and not be found out in the subsequent trial.

The series serves as a conclusion to the storyline of Hope's Peak Academy, the elite school where the Super High School Level Despair, Junko Enoshima, played hostess to a "killing school life" among its students under the guise of the evil bear Monokuma.