After being jailed for solving another mystery, the Mystery Inc. gang stumbles upon another mystery: a gruesome monster lurking underneath the town and cocooning everyone who comes near in green goop.

Strange things continue happening in Crystal Cove, when doorknobs suddenly vanish and a priceless diamond is hidden somewhere. To top it all off, a mysterious Ghost Trucker is also scaring the town.

A Man Crab attacks Crystal Cove beach during a volleyball tournament for Trickell's Triquid diet mixture. The gang must stop him and solve this mystery before the tournament's female players, who the Man Crab has taken a liking to, are put in danger. Meanwhile, Velma gets some relationship advice from Daphne.

The gang attends the Royal Knights Faire in Crystal Cove, but so does an unexpected guest. A scary-looking gnome is paralyzing everyone wearing pirate costumes at the faire.

When two giant monsters start to attack Crystal Cove, Mayor Jones asks Fred and the gang to help him and the sheriff capture them. Meanwhile, Shaggy has to choose between his relationship with Velma and his friendship with Scooby.

When Fred invites the gang on his and Daphne's second date, it pushes Daphne into the arms of Obnarb, the leader of an Orc Biker group called the Wild Brood who have come into town. When a break in at the armory happens and a dangerous weapon is stolen, the Wild Brood are the top suspects. It's up to the gang to solve this mystery, save the Wild Brood, and find the imposter Orc Biker.

When Mayor Jones buys online an ancient Persian temple, in order to boost business in Crystal Cove's amusement Park, "Creepy Spooky Terror Land", he never thought that that temple would come with a Manticore, a vicious mythological animal, who is been eating the park's visitors. Having no other option, he asks Fred and the gang to help him capture the beast, and while they do it, he does some snooping around, regarding the mysterious puzzle piece that the gang found in Darrow Mansion.

A high-tech creature called Obliteratrix attacks the gang and forces them to investigate the case of the haunted treasure with the help of H.P. Hatecraft.

The gang finally follows the trail to find the hidden treasure, but they didn't think The Freak would go after them. On the other hand, many truths are revealed, including the goal of Professor Pericles and the true identity of Fred's parents. And as if that were not enough, the gang faces a big problem when the parents get angry due to the behavior of their sons. And just when the mystery of the town is at its highest level, does this mean the end of the gang or the beginning of a new problem?

Velma and Hot Dog Water go to Russia on a mission for Mr E, and bring back an old house which springs legs and runs rampage over town. Meanwhile the gang are looking to replace Daphne and Velma suggests Hot Dog Water.

Fred tries to get Daphne back. Crybaby Clown returns to rob Crystal Cove and kidnaps Daphne as well. Daphne is rescued and agrees to return to the gang. Mr. E tries to re-recruit Angel Dynamite.

Dreamweaver has come to life brainwashing an old group of Crypts and Creepers players (including Sheriff Bronson Stone) by entering their minds while they sleep!

A creature called The Hodag of Horror attacks Crystal Cove; meanwhile, Brad Chiles and Judy Reeves (Fred’s real parents) have suddenly appeared along with a dog whom Scooby has taken a fancy to.

An artist's painting comes to life and attacks patrons of the museum. The gang is asked to solve the mystery so the Art Museum can be saved.

A bear-like creature attacks Mayor Nettles and Sheriff Stone in the Crystal Cove woods near Destroido. They turn to the gang for help, explaining that the creature is called the Scarebear and has been stalking the grounds near the Destroido company for weeks. The gang finds out that the Destroido company has allowed toxic lithium to spill into the woods, which has resulted in the mutations of inhabitant plants and creatures including the Scarebear. Meanwhile, Mr. E and Professor Pericles have recruited Brad and Judy to help them find the gang's pieces of the Planispheric Disk, and have resorted to drastic measures to get the gang out of the way.

An evil goat man named Krampus sends the gang on a quest.

Dr. Zin wreaks havoc on Crystal Cove.

The Crystal Cove Haunted Historical Society performs reenactments of Crystal Cove history every year. During a rehearsal for this year's production, a Phantom Mummy resembling one of the props scares off the cast and crew members. Vincent Van Ghoul, called upon to take over production, finds the set destroyed and calls in Mystery Incorporated, who become the new cast and crew for the play. Meanwhile, Professor Pericles recruits Brad and Judy to steal the Planispheric Disk back from the gang.

Professor Pericles creates a herd of mutant cattle to destroy Crystal Cove in an attempt to locate the Planispheric Disk.

A monster appears in the middle of Francilee Jackson's cooking show; Dr Rick Spartan helps the gang find out what's going on.

Professor Pericles tries to find the entrance into the caverns where the cursed treasure and the evil entity are buried.

Our heroes travel through the underground caverns.