The narrative begins with the protagonist, Misuzu, a dedicated researcher and mother, grappling with a severe demographic crisis: humanity faces extinction due to a drastic imbalance in the male-to-female population ratio, with males now comprising less than 20% and possessing diminished reproductive capabilities. This situation necessitates reliance on sperm banks for artificial insemination, a system further strained by the recent death of the last remaining young male with superior genes. Misuzu is spearheading the "Harem Project," officially the "Natural Reproduction Promotion Project," aimed at reversing this trend by encouraging natural reproduction and utilizing males with superior genes. However, a critical obstacle arises: all tested males possess inferior genes, rendering them unsuitable for the project.
Misuzu's dedication to her work has severely damaged her relationship with her son, Yuuto, whom she raised with an intense focus on an elite education, inadvertently making him withdrawn and hesitant in social interactions. Her junior, Ayumi Kanzaki, who also serves as the chairperson of the prestigious Renrei Joshi Gakuen (a girls' academy), suggests Misuzu review Yuuto's medical data. To her astonishment, Yuuto possesses exceptionally strong genes and high reproductive capacity, making him the ideal candidate for the Harem Project. This discovery forces Misuzu to confront her past parenting choices and decide to place her son at the center of the project, a decision that will profoundly impact his future.
The story then shifts to a flashback detailing Misuzu's past. During her university research on population decline, she met Naoto Takanashi. He initially approached her with simple gifts of food, concerned about her well-being as she often slept in the lab. Their relationship developed from this unusual beginning, and they eventually moved in together, married, and had a son, Yuuto. Naoto's subsequent assignment overseas for a project led to their separation, with Misuzu remaining in Japan to raise Yuuto. Her demanding career, however, led to a strained relationship with her son, mirroring the sacrifices she made for her work.
Yuuto, now a middle school student, is informed by his mother that he will be transferring to Renrei Joshi Gakuen, a prestigious all-girls boarding school. This is part of the Harem Project, where he is intended to find a future spouse among the students. Yuuto is surprised and apprehensive, having been unaware of the project's true nature. Upon arriving at the academy, he meets the chairperson, Ayumi Kanzaki, who explains the project's goals: to increase the natural birth rate and prevent population decline by having Yuuto engage in romantic relationships with the female students. The students are unaware of this true purpose, believing they are simply attending a prestigious school.
Yuuto begins his life at the academy, facing the awkward reality of being the sole male student. He encounters various female students, including Arisa Kosaka, who is openly hostile towards him, and Mana Aigura, who expresses curiosity and a desire to understand his presence. Mana, whose family's cosmetic company, Hakuhodo, is struggling, sees the Harem Project as a potential opportunity.
During a school assembly, Chairperson Kanzaki officially announces the Harem Project to the entire student body. She reveals that all female students are potential candidates to become Yuuto's spouse, with the goal of fostering natural reproduction. Students who are not interested in participating are offered the option to transfer to other schools. This announcement causes a stir among the students, and Mana, after learning the truth, becomes determined to be chosen by Yuuto, seeing it as a chance to change her life. The project's revelation creates a competitive environment among the students, each vying to be selected by Yuuto.