"Blue Gender" is a science fiction manga series set in a dystopian future where humanity faces extinction due to the emergence of the Blue, insect-like alien creatures that have overrun Earth. The story begins with Yuji Kaido, a young man diagnosed with a rare disease, placed in cryogenic sleep in the late 20th century as a last resort for treatment. He awakens more than two centuries later to find the world drastically changed. Earth is no longer habitable for humans, who now live in a space station called Second Earth, orbiting the planet. The Blue have decimated most of humanity, and the remnants of civilization are engaged in a desperate struggle for survival.

Yuji is rescued by soldiers from Second Earth, led by Marlene Angel, a hardened and skilled warrior. Marlene and her team are part of the Armed Humanoids, advanced mecha units designed to combat the Blue. Yuji, initially disoriented and unprepared for the harsh realities of this new world, is forced to adapt quickly. His awakening is significant, as he is believed to hold the key to humanity's survival due to his unique genetic makeup, which may provide a way to combat the Blue.

As the story progresses, Yuji and Marlene form a complex relationship, with Yuji's idealism and humanity contrasting sharply with Marlene's pragmatic and battle-hardened demeanor. The narrative explores their journey across the ravaged Earth, encountering other survivors, rogue factions, and the relentless Blue. The series delves into themes of survival, the cost of war, and the ethical dilemmas of genetic experimentation, as Second Earth's leadership pursues controversial methods to ensure humanity's future.

The plot thickens as Yuji discovers the true nature of the Blue and their connection to humanity. The Blue are revealed to be the result of human genetic experiments gone awry, a consequence of humanity's attempts to evolve and adapt to environmental changes. This revelation forces Yuji and Marlene to confront the moral implications of their fight and the possibility of coexistence with the Blue.

The series builds toward a climactic confrontation between the remnants of humanity and the Blue, with Yuji and Marlene at the center of the conflict. Their choices and actions ultimately determine the fate of both species, leading to a resolution that questions the boundaries of humanity and the price of survival in a world forever altered by hubris and desperation.