The game takes place in a different universe from the existing Professor Layton and Ace Attorney universes. Both Professor Layton and Phoenix Wright find themselves in a different world from their own, where they find the strange medieval city known as Labyrinth City has been victim to a number of impossible occurrences recently and like in the Ace Attorney universe where magic is real. The town is home to witches who hide in the shadows, and is controlled by an evil villain known as the Story Teller.