One summer afternoon, Shawn goes for a drive with his parents and dog, Ace, but the family car suffers a flat tire in front of an abandoned mansion. Ace is upset by something inside the mansion and leaps out of the car to investigate. Shawn's parents follow Ace, but fail to return. As Shawn tentatively approaches the dilapidated structure, the entrance door swings open, and he's drawn into a magical vortex. Reunited with Ace, Shawn must travel into the heart of the Deep Labyrinth to rescue his parents.

There is also a second story of another man who gets sucked into a warphole while talking on his cellphone. He finds himself trapped in a labyrinth. As he journeys through, he is forced to reconcile the past, and realize what it is that traps him in the labyrinth.

Each scenario has multiple endings based on the actions and performance of the player, as well as helpful items sequential playthroughs, to aid unlocking all the secrets of the labyrinth.