The Player starts the game in their new cottage on the Oregon coast. According to the Players diary, he/she (personal effects in the new cottage, such as a handbag, suggest a female protagonist, but the gender is never explicitly defined) is a struggling writer who has just moved in, and recently met his/her eccentric next door neighbor, Dr. Jeremiah Krick, and his daughter Amanda, who live in a nearby lighthouse. Glancing out of the window, he/she sees the lighthouse struck by lightning and, afterwards, begin to glow strangely. On the Player's answering machine, Dr. Krick has left a frantic message begging the player to come over to his house and watch Amanda.
Upon arriving at Dr. Kricks house, the Player discovers the front door locked, darkness inside, and silence. After turning on the power and entering, the Player finds Amanda in her crib, alone. Once the player has explored the house, a snap is heard, and Amanda begins crying. When the Player enters her room, the "Dark Being", described in Dr. Kricks journal, takes Amanda, and jumps through a portal. At this point, the Player can either follow him through, or use Dr. Kricks laboratory to construct their own portal. Either way, the Player ends up on a rocky beach in a parallel world. Krick's notes on this make reference to the real physical concept of Godel's universe
As the Player explores 6 different locations in the parallel world, the goal becomes clear. He/she must build an Ionising Cannon, whose 7 pieces are scattered between the different locations. Then, the Player must use this cannon to capture the Dark Being, and save Dr. Krick and Amanda.
GameSpot's first game guide was for Lighthouse.