Scooby-Doo Mystery is a point-and-press adventure featuring two playable episodes of a typical Scooby-Doo cartoon.
The story follows Daphne's Uncle Blake, who invites the gang to his hotel for a ski weekend. However, they soon discover that the ghost of the Ancient Chieftan is haunting the hotel due to a construction project on his burial grounds. After Uncle Blake goes missing, it's up to Scooby and Shaggy to find clues and solve the mystery.
The game also features another episode at the Ha Ha Carnival, where Fred, Daphne, and Velma get trapped in a pond, and a phantom clown starts chasing Scooby and Shaggy. Both episodes involve collecting clues, solving puzzles, and avoiding obstacles as Scooby and Shaggy work together to uncover the truth.
The gameplay involves walking around the environments and choosing actions from menus to interact with objects. Players can also save their progress using a password feature, allowing them to continue where they left off.