"Danganronpa 3: The End of Hope's Peak High School: Zetsubō Hen" serves as a prequel to the events of the "Danganronpa" series, exploring the origins of the tragedy that led to the collapse of Hope's Peak Academy. The story is set in the prestigious Hope's Peak Academy, an institution that gathers the most talented students, known as "Ultimates," to nurture their abilities. The narrative focuses on Class 77-B, a group of students who become entangled in a series of escalating conflicts and psychological manipulation.

The series begins with the arrival of Makoto Naegi's sister, Komaru Naegi, who is introduced to Class 77-B as a new student. The class is led by their homeroom teacher, Chisa Yukizome, who strives to foster unity and hope among her students. However, tensions arise as the students grapple with their personal struggles and the pressures of being Ultimates. Among the central figures are Hajime Hinata, a reserved and uncertain student, and Nagito Komaeda, whose erratic behavior and obsession with hope and despair create friction within the group.

As the story progresses, the students are drawn into a sinister experiment orchestrated by the enigmatic Junko Enoshima, the Ultimate Despair. Junko manipulates the class, exploiting their insecurities and pushing them toward despair. Her influence leads to the breakdown of trust among the students, culminating in a series of tragic events that transform them into the Remnants of Despair, a group responsible for widespread chaos and destruction.

The narrative also delves into the origins of the Future Foundation, an organization formed to combat the despair caused by Junko and her followers. Key members, including Kyosuke Munakata, Juzo Sakakura, and Chisa Yukizome, are depicted as they navigate their roles in the escalating crisis. The series highlights the ideological clash between hope and despair, with characters like Hajime Hinata and Nagito Komaeda embodying these opposing forces.

"Danganronpa 3: Zetsubō Hen" intertwines its plot with the events of "Danganronpa 2: Goodbye Despair," providing context for the characters' motivations and actions in that game. The series concludes with the fall of Hope's Peak Academy and the rise of the Remnants of Despair, setting the stage for the events of the mainline "Danganronpa" games. Through its exploration of psychological manipulation, moral ambiguity, and the consequences of extreme ideologies, the series serves as a crucial piece of the "Danganronpa" narrative, offering insight into the origins of its central conflict.