Set in the year 2000, Penumbra: Overture follows the story of Philip, a thirty-year-old physicist whose mother recently died. After receiving a mysterious letter from his supposedly dead father, Philip follows a series of clues that lead to him to a mysterious location in uninhabited northern Greenland. The harsh cold forces him to take shelter in an abandoned mine. Unfortunately, the mine's entrance collapses as he enters it, and he is forced to move deeper inside. Within the mine, Philip discovers diary extracts written by a scientist of some sort, who was alone and gradually resorted to eating cave-dwelling spiders as an alternative food source as his supplies diminished.