The Mystery of the Mary Celeste is a hidden object game with adventure elements. The objective is to collect all the items shown at the bottom, as a series of black-and-white images on porthole windows, and use them to solve puzzles. Some portions of the scenery bring up a close-up window showing another angle of the scene, usually containing some of the required objects. Clicking on certain objects and characters opens up a number of connected containers around them, and the player has to drag and drop the collected tools from the inventory portholes to these blue circles, to complete the scene and move to the next one.

Mini-games usually appear at the end of each chapter, presenting various challenges and puzzles. A pipeline has to be reassembled with scattered pieces, lengths of rope must be untangled by dragging a series of pulleys, wires have to be connected to complete a circuit, red pins have to be fixed to a nautical map following a list of coordinates and a radio has to be tuned to the correct sound waves. The games can be skipped at any time.

Fighting her fears of drowning, Mary Morehouse embarks in the maiden voyage of the Mary Celeste. While busy exploring the ship and following strange noises, the crew and passengers vanish, leaving her and the captain to solve the mystery surrounding their disappearance.