Coppelion takes place 20 years after a 2016 nuclear power plant meltdown in Tokyo, which left the city uninhabitable due to high radiation levels. The area is now a ghost town, prompting a distress signal that leads the Self Defense forces to deploy three members of the Coppelion unit, a special task force. Despite the hazardous environment, the girls are not equipped with protective gear. Their mission is to search for any remaining survivors in the contaminated zone.