In the year 2999, only eleven cities still survive on Earth. The climate has changed drastically, and a biochemical apocalypse has made women extinct. For centuries, the male population of Earth has survived by depending on only one woman, called the Holy Mother, whose ova are harvested to create genetically engineered children. By now, any concept of a world in which women exist as ordinary people is long gone. Society has re-structured itself around all-male families, and relationships between men and adolescent boys have become the norm.

At the beginning of Marginal, the Holy Mother is assassinated by a terrorist known as Grinja. The government in power doesn't want to start a mass panic, so it pretends that the Holy Mother has only shed her vessel, and that she will be miraculously "reborn" in the near future. The public, which is superstitious and devout, believes this easily. Only government officials know that behind the scenes, there is a frantic effort to create a being able to give birth.

The manga's story revolves around Kira, who becomes involved in a three-way relationship with Grinja, the aforementioned terrorist, and Ashijin, a young man who calls himself Kira's owner. A complex plot and flawless world-building make the story irresistible, and Kira's search for freedom is as symbolic as it is gripping.