The player controls Norville "Shaggy" Rogers as well as Scooby Doo simultaneously (he automatically mimics any movements that the player makes as Shaggy) making gameplay unique. The object of the game is to find clues to solve the 4 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 level Monster. Each of these will add to the players "Fright Meter" which, if full, will result in the player losing a life. Once enough clues have been gathered, Velma will send you to Fred to help him build a trap to catch the monster. The player then has to lure the monster to the trap before the end of level cutscene plays. At the beginning of each level, only a small portion will be accessible, but as more clues are found, more of the level can be explored. Between each case, a game clip of the Mystery Machine driving along with on-screen dialogue from the gang inside is shown. The mysteries themselves don't have much plot before or after each case, and the person in the monster suit is usually never met until they are unmasked.
The other three members of Mystery Inc. are there to help solve the case as well, though they are not playable. They do each serve a specific task however:
Fred Jones - The leader of the group, he will usually provide information on the mystery as well as help Shaggy and Scooby open locked doors. At the end of each mystery, the player must find specific items which Fred will use to build a trap to catch the monster.
Daphne Blake - The beauty of the group, Daphne may not help with the case itself, but she will provide Shaggy and Scooby with a supply of Scooby Snacks which will help keeps the players "Fright Meter" down. She will only give a Scooby Snack if the player has found enough clues.
Velma Dinkley - The implied lesbian of the group, the player must bring any clues they find to her for analysis. Each clue adds to the players point total which will give them a life for gaining enough of them.
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 - This is the Red Ryan which 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 parks janitor.
- Abandoned Ranch - 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.
- Haunted House - A house belonging to Daphne's Uncle which is being haunted by a 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 the kitchen area. In this level, the player controls Scooby Doo who is standing on his hind legs holding a slice of bread in each hand. Shaggy is behind him in a refrigerator with his back to the screen. Shaggy throws food items out which the player must catch by moving Scooby side to side. 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 a Scooby Bonus.
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 "Whack a Mole" with a mallet on three vases. The player must use the directional buttons to tell Shaggy where to swing. 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 in the time limit, they receive a Scooby Bonus.
Sega Mega Drive Version
This version is a Graphic adventure game divided into two scenarios: "Blake's Hotel" and "Ha Ha Carnival". The player controls Norville "Shaggy" Rogers as well as Scooby Doo simultaneously (he automatically mimics certain movements that the player makes as Shaggy, but sometimes strays) while Fred, Daphne and Velma make appearances in video sequences (often at the beginning and end of a mystery). The object of the game is solve puzzles to progress, uncover the mystery and catch the monster/criminal to win the scenario. The player has ten different actions to control Shaggy and solve puzzles. The action menu can be switched to the inventory menu to interact with the items and put them to use. Most of the puzzles require logic to solve, while others require a specific action to solve.
The gang goes to Daphne's Uncle Blake's hotel where a ghost of a Native American Chieftain has been scaring away clients and staff, with only the gardener and the cook remaining. While the gang goes to investigate, Shaggy and Scooby go inside the hotel only to find Blake has been kidnapped. Eventually Shaggy and Scooby come across a gold mine under the hotel and the heart of the mystery is revealed to be an ancient medallion the ghost is looking for.
Ha Ha Carnival
The gang goes to the Ha Ha Carnival which happens to be closed. An evil clown has sabotaged the services and imprisoned the carnival manager. Shaggy and Scooby help the manager and rescue the others stranded in a lake. After trying out all the rides, Shaggy and Scooby find out that the clown has a prime interest in getting employment in the carnival but was immediately rejected by the manager and proceed to capture him.
- Scooby-Doo Mystery at MobyGames
- Scooby-Doo Mystery at UK GameSpot
- Scooby-Doo Mystery at UK GameSpot
- Scooby-Doo Mystery from IGN