These are the villains that appeared in the show.
The evil leader of all Annunakki and the main antagonist of the whole series.
The Freak of Crystal Cove is one of the shows main antagonists along side Professor Pericles. He threatened The Original Mystery Incorporated to give up mystery solving or their families get hurt. 20 years later he resurfaces to see Fred Jones ignore Angel Dynamite's warning about him and then he pursues the gang for the Planespheric Disk and pieces to the cursed treasure. After fleeing out of The Caves, he is apprehended by Fred and as he unmasks the Freak, it is shown to be the Mayor. The Mayor confesses that he was never Fred's father all along.
The Slime Mutant is the first villian that the gang encounters in "Beware the Beast from Below." Its appearance was a tall green monster who smelled like Fruitmeyer's dessert. It is revealed at the end that the monster was Professer Emmanuel Raffalo, a Crystal Cove High teacher who used a secret door in Fruitmeyer's backroom to get into the sewers to drill a passage to get into the bank secretly.
Grady, Greta, and Gunter Gator, or the Gator Family appeared in Creeping Creatures. They were scaring people away from Gatorsburg to make sure no one found out that they were making faux gator products. Greta and Gunter run the hotel and Grady is a mechanic.
Rung Ladderton, was the rich owner of a ladder company, in Crystal Cove. who Daphne's parents wanted her to date. But it turned out that he was actually the ghost trucker, who'd been stealing glass doorknobs all around Crystal Cove, in an attempt to get rich.
It kidnaps people at a volley ball tournament.
The phantom spectre was a disguise used by Daniel Prezette, also known as Fantzee Pantz. He used this disguise, to try and take the Hex Girls down, for getting rid of his own career.
he paralyzes people dreesed as pirates at the medevil fair
The Humongonauts were the twin brother Max Minner and Jax Minner. They used the disguises to attack places that were owned by their brother.
The Frighthound was a creation the Mrs. Wyatt invented to tear the gang apart and let her son Jason be with Velma, but when she saw that they were blaming Jason for being the creator of the Frighthound, she decided to kill them all.
Sheila Altoonian was a close friend to Daphne's mum, Nan. she was eventually found to be the vampire in the episode: The secret serum. She was unhappy about how youthful Nan Blake was, and set out to find the ingredients of a youth juice formula from a Halloween magazine, so that she could gain the same kind of youthful look and the eternal beauty of a vampire.
Char Gar Gothakon, is the main character in a horror book wrote by H.P Hatecraft. In the episode:The shrieking madness the monster became a disguise that Howard E Roberts used to try and defend Hatecraft against his critics, but only ended up trying to get rid of the author.
The Cicada Creature was a monster by Grandma Moonbeam, she wanted to get rid of all the Destroido workers because they put landfill waste in her originally healthy nature slivers.
Lord Infernacus was the disguise of the funky phantom in Scooby's dream, he was using it to form a team of sidekicks and ship off all the human mystery solvers to South Africa, where there was apparently a desperate need for mystery solvers.
Shovel Nose or the shadow orc, was a disguise used by Maxwell to try and stop the shipment of a new games console, that had been designed by his co-workers.
Aphrodite, the goddess of love, was used by an a former student from Crystal Cove high to try and take her prom crown, after being mocked by her fellow students ages before. She used a love potion to make everyone in Crystal Cove fall madly in love with each other, that had been given to her by Professor Pericles.
The White Wizard was a disguise used by Mr Wong, a Chinese diplomat who came to Crystal Cove, looking for the fourth and final ring that he needed to open up a jade dragon and obtain the dragon's heart.
Nightfright was originally the name of a horror movie that was going to start production in Crystal Cove, but when Vincent Van Ghoul had to pull out, the director Argus Fentonpoof decided to use the idea of Night Fright to try and scare Vincent, as well as his two guests; Scooby and Shaggy live on TV, to try and prove that Nightfright deserved his own horror movie.
The Fish freaks
The fish freaks, were the disguises of Ernesto and his gang of protestors in the season 1 episode; the siren's song. They were using these disguises to try and keep people away from a haunted oil platform, where they were trying to mine for oil so they could make enough money to protest against it.
Crybaby Clown was an evil man-baby clown, who was terrorizing Crystal Cove at the start of season 2. He turned out to be the disguise of Baylor Hotner, a famous Hollywood thesbian, who'd come to Crystal Cove to do research for his next film. In doing so he masqueraded as Crybaby clown and kidnapped several Crystal Cover citizens, including Daphne. He was ultimately planning to take them to his special clown town until Fred and the rest of the gang stopped him.
The Baba Yaga was a diguise of Curator Vronsky.
Dreamweaver was the guise used by Horbert Feist when he attacked people in their dreams
The Hodag of horror
The Hodag was supposedly the main attraction of Jean Shepards's curio wagon, but was actually a disguise for Ned Fussbuster's trained monkey, Roberto, who he used to help him steal all kinds of expensive jewelry.
Junk was a masterpiece created by Andy Warsaw, which came to life and started attacking people, it turned 3people into gold, making them look like a famous painting. In the end it turned out that Butch Furbanks a member of Andy Warsaw's band had used Junk to try and get revenge on Andy for turning him into a pop star.
The graveyard ghoul
the graveyard ghoul was a disguise used by Count Evallo von Meanskrieg, to try and scare people off so he could mine for gas in the Crystal Cove cemetery.
Dark Lilith was the second disguise used by Hotdog water, this time to help Mr E find the fifth piece of the planespheric disc.
The fiend was a nightmarish Anubis like creature that was the disguise of Dan Flunk, He used it and his special nightmare giving firewood to try and close down the Burlington library, so he could go on holiday.
The Scarebear was supposedly a giant mutant bear that was wondering around the toxic swamp near Destroido. However it turned out to be the disguise of Benson Furman, a security guard at Destroido and former customer who had suffered a major side effect of one of their products and used the Scarebear disguise to take revenge on them.