Blue Gender takes set in the not-too-distant future, in a world where mankind has suffered greatly. The Blue, a species of bug-like aliens that invaded Earth and pushed humanity aside, have supplanted humans at the top of the food chain. Second Earth, a space station, has been built as a safe haven for mankind in the hopes of one day regaining the Earth. Yuji Kaido had been cryogenically frozen due to a condition known as B-Cells. When he awakens, he joins a group of troops who have come to Earth to rescue him. Unfortunately, nothing goes as planned on their journey return to Second Earth.