Most of the puzzles require logic to solve, while others require a specific action to solve. The action menu can be switched to the inventory menu to interact with the items and put them to use. The player has ten different commands located at the bottom of the screen to control Shaggy and solve puzzles.

The object of the game is to solve puzzles to progress, uncover the mystery and catch the monster/criminal to win the scenario. The player controls Norville 'Shaggy' Rogers, who is followed around by Scooby, while Fred, Daphne, and Velma make brief appearances, often at the beginning and end of a mystery. This version is a more traditional graphic adventure game divided into two scenarios: 'Blake's Hotel' and 'Ha-Ha Carnival'.

In both games, players take control of Shaggy Rogers and Scooby-Doo, who help solve various mysteries with other members of Mystery Incorporated who serve minor roles during gameplay. Both were released only in North America.

The other title, released for the Super Nintendo Entertainment System, is an adventure game with platforming elements. One of the games was released for the Sega Genesis and features a more traditional adventure game-style interface. Scooby-Doo Mystery is the name of two video games released by Acclaim Entertainment and Sunsoft in 1995 based on the Scooby-Doo animated series.

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