
Velma analyzes clues brought to her that help unravel the mystery and give the players clue points. Daphne periodically gives the duo Scooby Snacks that decrease the fright meter. Shaggy and Scooby can talk with various members of Mystery Incorporated during the game. 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. Each of these will add to the players "Fright Meter" which, if full, will result in the player losing a life.

In addition, the player must avoid hazards such as small creatures, falls from high areas, or the main monster of each level. If the player accumulates 10,000 points, they will receive an extra life. These clues give the players Mystery points and more points can be earned in the bonus levels. 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. The object of the game is to find clues to solve each of the four mysteries in the game. Each of the game's four levels starts with a cutscene of the Mystery Machine van driving along with the characters setting up the next mystery.

The player controls Shaggy Rogers, who is followed by Scooby-Doo.
