After the battle for the subterranean city of Genesis the surface people settle into an uneasy partnership with its inhabitants as they re-build the damaged city. This existence is soon threatened however by a rapidly spreading plague that is being carried westward across the Channel by refugees from Europe. With the possibility of the plague reaching Genesis within weeks, Alex and Elaine lead a medical team onto the surface to collect specimens from these survivors in the hope of finding a cure.

Within days however their convoy is attacked, and they discover that these refugees are not what they seem. They call themselves Alphas and far from being weak and diseased, these people have been genetically altered by the disease and consider they are the rightful inheritors of this post-apocalyptic world. When they discover the existence of Genesis with its advanced technology, they are determined to conquer the city and take the technology. Alex and Elaine face a race against time to find a cure to the Alpha plague and stop the Alpha army sweeping across the land, attacking Genesis and assimilating its inhabitants.