"World’s End Harem" is set in a dystopian future where a deadly virus known as the Male-Killing Virus (MK Virus) has wiped out nearly all men on Earth, leaving women as the dominant population. The story centers on Reito Mizuhara, a young man who was cryogenically preserved five years prior to the outbreak due to a terminal illness. Upon awakening, Reito discovers the world has drastically changed, with men now being a rare and valuable resource. Women, desperate to repopulate, seek out the few surviving men to serve as breeding partners.

Reito is placed under the care of a government facility where he is expected to participate in a program designed to repopulate humanity. However, he refuses to comply, driven by his unwavering love for his childhood friend, Erisa Tachibana, who was also cryogenically preserved but remains missing. Reito’s determination to find Erisa sets him apart from other male survivors, who often succumb to the pressures of their new roles. His resistance to the system creates tension with the authorities and the women assigned to monitor him, including the stoic and calculating Mira Suou, who oversees his care.

The narrative explores the ethical and societal implications of a world dominated by women, where men are treated as commodities. Themes of power dynamics, consent, and the consequences of a gender-imbalanced society are woven into the plot. Reito’s journey is marked by his struggle to maintain his autonomy while navigating a world that views him as a tool for survival. Alongside Reito, other male survivors, such as the charismatic and morally ambiguous Elisa Tachibana, play significant roles in shaping the story, each representing different responses to their newfound status.

The series delves into the personal motivations of its characters, particularly the women who are tasked with managing the male survivors. Mira Suou, for instance, is portrayed as a complex figure whose loyalty to the system is tested by her interactions with Reito. The story also introduces a shadowy organization known as the "Five Leaves," which seeks to exploit the chaos for its own agenda, adding layers of intrigue and conflict.

"World’s End Harem" balances its dystopian premise with elements of romance, drama, and suspense, creating a narrative that examines the fragility of societal structures and the resilience of human relationships. The series raises questions about identity, morality, and the lengths to which individuals will go to preserve their humanity in a world transformed by catastrophe.