Lux-Pain is set in historical Kisaragi City, a town plagued by mysteries from small mishaps to murders - with no logical explanation as to why these events occur. It seems “Silent”, a worm born through hate and sadness, has infected humans and forced them to commit atrocious crimes. The hero's parents are victims of such crimes. To avenge his parents, Atsuki goes through a dangerous operation to acquire Lux-Pain in his left arm, a power so strong that his left eye turns golden when using it to seek and destroy Silent for good.

• Investigate your surroundings and gather hints by conversing with characters in the game
• Explore the massive world of Kisaragi City
• Use your stylus to conduct autopsies of Silent worms found throughout the game
• Psychic Powers enable you to save potential victims from Silent. Use your stylus to find the parasite before it reaches the heart of the victim.

I byen Kisaragi City er ingen trygge. Avskylige parasitter som kalles SILENT infiserer mennesker og tar kontroll over hjernen deres. De menneskene som blir infisert begår de mest grusomme mord og sprer frykt hvor enn de ferdes. Heldigvis har en organisasjon som går under navnet FORT etablert seg med én hensikt; å ta rotta på parasitene. En av deres medlemmer, Atsuki, har det for seg at han kan se SILENT. Lux Pain minner om en japansk anime, men er samtidig mørkere og mye mer skremmende. Spillet passer derfor den litt eldre spiller.