The story follows Benjamin Briggs, the historic captain of the Mary Celeste. In 1872, the ship was found empty, and the fate of Briggs and the rest of the crew remains a mystery. The game places Briggs in Limbo, where he must aid Destiny in a war against Fate.

Briggs is portrayed as having a fear of insects, and he must confront that fear to solve puzzles and move forward. The player is acknowledged by the characters as a “spirit guide,” and Briggs sometimes complains to the player about his surroundings and the tasks he is given.

During the final sequence, the player rather than Briggs becomes the puzzle-solving protagonist. If the player does not move the mouse for a period of time, Briggs will comment on it.