Lux-Pain is a video game set in historical Kisaragi City, where mysterious events ranging from small mishaps to murders occur without explanation. It turns out these are the result of Silent, an evil worm born from hate and sadness which has infected humans and made them commit atrocious crimes. The protagonist Atsuki's parents were victims of this, so he decides to avenge them by undergoing a dangerous operation that gives him Lux-Pain - a powerful force that manifests as his left eye turning golden when used for seeking out and destroying Silent once and for all.