Qualidea Code takes place in a post-apocalyptic Japan where children were cryogenically frozen to protect them from the Unknown, extradimensional beings that launched a devastating attack on humanity. The frozen children are thawed out when humanity establishes a stronghold in a corner of the country, where they discover they've developed supernatural powers known as Worlds. These powers are wielded by the six most powerful children, who lead their respective cities in a desperate defense against the Unknown.