Unlike its SNES counterpart, the Genesis version of Scooby-Doo Mystery is a point-and-click (or point-and-press button rather) adventure featuring two playable episodes of a typical scooby-doo cartoon.

Blake's Hotel - Daphne's Uncle Blake has invited the gang over to his hotel for a ski weekend. Upon reaching the hotel they learn that the ghost of the Ancient Chieftan is scaring all the customers away, as he isnt happy about a hotel being built on his burial grounds. Soon Uncle Blake is kidnapped, and its up to Scooby and Shaggy to find clues and hunt this ghost down.

Ha Ha Carnival - The gang arrives at an almost-deserted carvinal, looking for some fun. Soon enough Fred, Daphne and Velma get trapped in a pond when they go out in one of the rides. Not only that, someone has broken the rollercoaster tracks. Then an evil looking phantom clown has Scooby and Shaggy being chased all around the carnival. Another mystery for the pair to solve.

Both mysteries have Scooby and Shaggy on their own, collecting clues and putting them together. You control Shaggy mostly while Scooby just keeps him company. The game interface involves walking around and/or choosing actions from a menu and using them with objects. A password feature is provided so you can continue where you left off.