In Qualidea Code, the sky tears open and the extradimensional beings known as the Unknown launch a sudden, brutal attack on humanity. In response, Japan places all of its children into cryogenic sleep, hoping to shield them until the war can be fought to the end.
Years later, humanity has managed to hold a foothold in a corner of Japan, which now serves as the frontline of the conflict. When the children awaken, they discover that they developed Worlds during cryogenesis: supernatural powers unique to each person. The six most powerful children are assigned to command the reclaimed cities and use those abilities to defend the strongholds against the ongoing invasion. Childhood friends Ichiya Suzaku and Canaria Utara lead Tokyo, siblings Kasumi and Asuha Chigusa manage Chiba, and Maihime Tenkawa and Hotaru Rindou oversee Kanagawa.
As the Unknown continue to attack with unsettling regularity, the city heads and their subheads fall into constant friction, turning even routine defense into a series of petty rivalries and arguments. When the pressure from the Unknown suddenly increases, the three cities must set aside their differences and fight together, or humanity risks losing its last line of defense.