Blue Gender takes place within the not too distant future during a world where things have gone terribly wrong for humanity. Humans are replaced at the highest of the organic phenomenon by the Blue, a race of bug-like aliens that have colonized Earth and pushed humans aside. an area station, Second Earth, has been constructed as a secure haven for humans, with the hope of 1 day reclaiming the world another time.
Yuji Kaido was cryogenically frozen, having been affected by a disease referred to as B-Cells. Once awakened, he joins a team of soldiers that have come to Earth to extract him. Unfortunately, nothing goes consistent with plan as they create their way back to Second Earth.
Yuji will need to affect the horrors of fighting a bloody war as he and therefore the fighters from Second Earth look to survive. Will they be ready to get back Earth without losing their humanity?