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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 van 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 gets 10,000 points, they will get an extra life.
In addition, the player must avoid hazards such as small creatures, falls from high areas, and 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 little portion of the level will be accessible, but as more clues are found, more areas can be accessed.
Shaggy and Scooby can talk with various members of Mystery Incorporated during the game. Daphne periodically gives the duo Scooby Snacks that decrease the fright meter. Velma analyzes clues brought to her that help unravel the mystery and give the players clue points. Once enough clues have been gathered, Velma will send Shaggy to Fred to help him build a trap to catch the monster using certain items the player gathers. The player then has to lure the monster into the trap, thus capturing it so Fred and company can reveal its true identity.
There are four levels in the game, and the player receives a password after each one to allow them to return at any time.
- Spooky Shipwreck — The Red Ryan ship is being haunted by a ghostly pirate named "One-Eyed Matt". He is actually after treasure on sunken ships nearby which he planned to melt down and steal.
- Haunted Amusement Park — The Fun Fair is being haunted by an Evil Clown who seeks to close the park as revenge for being fired when he was the park's janitor.
- Spooky Swamp — The Tar Monster is scaring everyone away from this ranch in order to buy the land cheap and then sell it at a profit due to it containing valuable minerals.
- Bradshaw Manor — A Mansion belonging to Daphne's Uncle which is being haunted by an evil vampire named Count Bagosi. He is trying to scare everyone away to protect his illegal counterfeiting operation.
There are two bonus levels hidden in each mystery. The first is found in kitchen areas. In this level, the player moves Scooby, from side to side, catching food items that Shaggy is throwing from the refrigerator onto slices of bread. The food stacks up as it is caught but if Scooby moves too fast some of it will fall. If the sandwich is large enough, then the player will be awarded with bonus points.
The second is found randomly in each level, but usually appears upon entering a new area of the level. On this level, Shaggy plays a game of "Whac-A-Mole" style with a mallet on three vases. The object is to hit as many monsters (ghosts, vampires, knights, etc.) as possible without hitting Scooby or the other members of the gang. Points are added for monsters hits and subtracted for hits to friends. Time Bonus, Time Freeze, and Speed Boost can also be collected from the vases to prolong the game and get more points. If the player scores enough points within the time limit, they receive a Scooby Bonus.
- Don Messick as Scooby-Doo
- Casey Kasem as Shaggy Rogers