The player uses Scooby-Doo to take down enemies and collect clues for Velma. Scooby-Doo can change costumes which can give him different moves such as kung-fu and fly like a bat. Many parts of levels require costumes, so costumes are essential to the progression of the game.
Scooby-Doo and the gang are visiting Fred's cousin Jed at his factory Monstrous Fright and Magic or M.F.M. Once they get there, Jed is missing, and his animatronics have gone haywire. Winslow Stanton tells them Jed is a thief and has stolen his mubber and animatronics. Scooby and the gang explore different areas in search of Jed. The go to Chinatown, The Guitar Ghoul's Theme Park, and a Museum, trying to solve a big mystery while solving the mystery of Jed's dissapearence.
Villains and characters
- Scooby-Doo - The famous Great Dane who has a cowardly streak a mile long. The player takes control of him throughout the game. He is voiced by Scott Innes.
- Shaggy Rogers - The always-hungry skinny dude accompanies Scooby on a few levels (only at the beginning). The player saves Shaggy in the Sewers, Water Park, Dinosaur Exhibit and Medieval Exhibit levels. Bringing food items to Shaggy can earn the player extra hit points. He is also voiced by Scott Innes.
- Fred Jones - He is looking for his cousin Jed, claiming that his cousin is not behind the attacks and thievery. He is kidnapped, along with Daphne, and caged in the Undersea Exhibit level. He is voiced by Frank Welker.
- Daphne Blake - The unlucky, yet beautiful, damsel in distress that gets captured in the Temple, Circus Tent, and Undersea Exhibit levels. She is voiced by Grey DeLisle.
- Velma Dinkley - When the player gathers clues, he/she takes them to Velma, who will evaluate the clues, and open up new areas in the hub. Velma hates to lose her glasses, but likes clues. She is voiced by Mindy Cohn.
- Winslow Stanton - Winslow is the creator of mubber, which can be shaped into anything. He accuses Jed of stealing his animatronics and mubber, sending Scooby and the gang to Chinatown, where Jed might be delivering things. He is voiced by Adam West.
- Marcy Stantom - Marcy is Winslow's wife and the woman who helped Stanton create mubber. Not much is known about her.
- Jed Jones - Jed is the lost cousin of Fred, and an employee of Monstrous Fright and Magic. He is voiced by Chris Edgerly.
- Zen Tuo (Scooby-Doo, Where Are You!: Mystery Mask Mix-Up) - A powerful spirit haunting Chinatown that controls a flying dragon. He will place a curse on anyone who defies him. He is voiced by Fred Tatasciore.
- Chinese Zombies - The ghostly henchmen of Zen Tuo.
- The Guitar Ghoul (The Scooby-Doo Show: The Diabolical Disc Demon) - A mysterious Rock Star whose ghost now allegedly haunts his rock'n'roll-themed amusement park. He is voiced by Chris Edgerly.
- The Caveman (Scooby-Doo, Where Are You!: Scooby's Night With a Frozen Fright) - A ghostly caveman who haunts the "Amuseum". He is voiced by Fred Tatasciore.
- Pterodactyl (The Scooby-Doo Show: Hang in There, Scooby-Doo)- The creation of an ancient pterodactyl. He is a common enemy featured in the amuseum levels. There are two versions of the Pterodactyl, a regular one which is green and an orange one that breathes fire. A giant Fire-Breathing Pterodactyl robot is the final boss. He is voiced byChris Edgerly.
- Fire Breathing Groupie - A mechanical woman that can breathe fire. They were originally used to star in the Guitar Ghoul's music and horror videos.
- The Ninja - Mysterious warriors that can appear out of nowhere, and throw shurikens.
- Jugglin' Clown (Scooby-Doo, Where Are You!: Bedlam in the Big Top) - A clown, who is a minion of the Guitar Ghoul, appearing in the theme park levels as a common enemy. Listed as "Juggling Clown" in credits, and voiced by Chris Edgerly.
- The Black Knight (Scooby-Doo, Where Are You!: What a Night for a Knight) - A ghost who haunts an old suit of armor. He is a common enemy in the museum levels, and is voiced by Fred Tatasciore.
- 10,000 Volt Ghost (The Scooby-Doo Show: Watt a Shocking Ghost) - A ghost made out of pure electrical energy. He is voiced by Chris Edgerly.
- Kung Fu Maiden is a robot that can stretch her hair a long distance. She also attacks by swinging her fan around to hit Scooby.
- The Beast of Bottomless Lake (The Scooby-Doo Show: The Beast is Awake in Bottomless Lake) - A lake monster that terrorized the Bottomless Lake Village in Canada. Jed is found trapped inside a mubber costume of the villain in the final level.
- Circus Strongman - Incredibly strong, These people were designed to do numerous tasks. They can also use their cymbals as weapons to cause major destruction and attack unsuspecting civilians.
In Scooby Doo! Unmasked, there are 5 worlds/levels that you play:
- World 1: Monstrous Fright and Magic- A movie studio which seems empty. Tutorial level and Easiest Level.
- World 2: Chinatown- An abandoned chinatown that is ruled by Zen Tuo and his Dragon that emits fireballs. Levels consist of Cookie Factory, Sewers, and Temple. The Boss Fight takes place on a Rooftop.
- World 3: Rock 'n' Roller Coaster Land- An amusement park which is ruled by the Guitar Ghoul, a rockstar who makes animatronics evil and can emit electrical pulses from his guitar. Levels consist of The Haunted House, Water Park, and Circus. The Boss fight takes place in the House of Mirror.
- World 4: Natural History Museum- An abandoned museum where monsters hide in exhibits and a cavemans lurks the grounds. Levels consist of The Dinosaur Exhibit, The Medievil Exhibit, and The Undersea Exhibit. The Boss Fight takes place in the Planetarium.
- World 5: Back To Monstrous Fright and Magic-(Final level)- Winslow Stanton and an army of mubber monsters have taken over the studio and factory. The level is the same as at the beginning except with more obstatcles. The final boss fight takes place on a city movie set.