The player controls Shaggy Rogers, who is followed by Scooby-Doo. Each of the game's four levels starts with a cutscene of the Mystery Machine driving along with the characters setting up the next mystery. The object of the game is to find clues to solve each of the four mysteries in the game. These clues can be obtained by finding them in the open, completing a specific task, or having Scooby "sniff out" hidden clues in each area. These clues give the players Mystery points and more points can be earned in the bonus levels. If the player accumulates 10,000 points, they will receive an extra life.
In addition, the player must avoid hazards such as small creatures, falls from high areas, or the main monster of each level. Each of these will add to the players "Fright Meter" which, if full, will result in the player losing a life. At the beginning of each level, only a small portion of the level will be accessible, but as more clues are found, more areas can be explored.