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.

The gang decides to launch an investigation into the existence of a mythical ghost town that is believed to have been populated by alligators.

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 children of Crystal Cove are being turned into monsters by a creature named Que Horrifico, scaring all of the adults in town. As a result, they abandon their children and run for their lives.

Fred becomes the target of a high school crush when new girl Alice May falls for him. However, Alice May is actually a ghost with a reputation for taking guys with her and making them disappear forever.

The Hex Girls (consists of Thorne, Dusk, and Luna), Velma's favorite band, come to Crystal Cove and plan to give the gang a concert. But things go awry when The Phantom, an evil specter, suddenly appears with the intention of permanently taking The Hex Girls out of the music business.

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.

A monster called the Fright Hound starts attacking Crystal Cove and people believe Scooby-Doo is behind it. Could Scooby be the one attacking the city or is someone setting him up?

There's a vampire loose in Crystal Cove, terrorizing the residents and stealing an odd assortment of loot. When the gang does some sniffing around, they discover an unlikely suspect… Daphne's MOTHER. Things are already strained within Mystery Inc., and with this latest blow, the gang is truly torn in half. Girls on one side, boys on the other.

With Mystery Inc. broken up, the gang decides to check out life after high school and spend a weekend at DARROW COLLEGE. But things don't go as planned when a creature called CHAR GAR GOTHAKON begins terrorizing the campus. Turns out this beast is a fictional character come to life. A creation of the author H.P. HATECRAFT who is a professor at the school.

The gang investigates after Crystal Cove begins suffering from an infestation of deadly insects that targets workers of the company Destroido, the company that makes Shaggy and Scooby's favorite snacks.

Sick in bed right before the big Mystery Solvers Club State Finals, Scooby dreams about going to the competition and teaming up with fellow mystery-solver sidekicks Speed Buggy, Jabberjaw, Captain Caveman and The Funky Phantom to rescue their friends from the clutches of the demonic Lord Infernicus.

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 the entire town of Crystal Cove is taken over by Aphrodite's love spell, only Scooby-Doo and the recently-escaped Professor Pericles can save the gang from the spell and solve the mystery. But does Professor Pericles have ulterior motives?

When the gang goes on a quest to find out what happened to the original Mystery Incorporated group on their last case of the 75 year old disappearance of the Darrow Family and their mansion, they find themselves trapped in the underground Darrow Mansion, which has been booby trapped. Will the gang solve the mystery and escape with their lives?

When an exchange student named Mai Le comes to Crystal Cove, she draws the affection of Shaggy. A dinner party hosted by the Blake Family is interrupted by the Red Wizard warning to stay away from the Dragon's Heart which he has sworn to protect at all cost. Later, Mai Le and the gang to come under attack by a White Wizard who is after Mai Le's ring, and the Red Wizard comes to the gang's rescue, but he is too late to save the ring. The Red Wizard turns out to be Mr. Chen, the owner of Chen's Internet Cafe and Tea House. He reveals that with the White Wizard, now in possession of all four rings, is able to open the Jade Dragon's Heart, which is a priceless ruby. Will the gang solve the mystery or is everything not as it seems?

Scooby and Shaggy win an essay contest to have dinner with Vincent Van Ghoul. They go to his mansion and are attacked by a monster who calls himself Nightfright. Shaggy calls the gang and the gang rushes over. The are chased by Nightfright and go into a room and lock the door. Fred makes a trap and asks Vincent to lure the monster into it. Finally, they catch Nightfright in Fred's trap. The end of the episode shows them eating dinner, Daphne devouring everything in sight because she has not eaten for hours.

Feeling left out of the group, Velma goes solo to investigate attacks by amphibious "Fish Freaks" in the area around an abandoned oil rig, only to find a friend of her own... in the form of a mermaid!

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.

When Fred's favorite adventurer, Dr. Rick Spartan, starts teaching biology at the Crystal Cove's High School, the gang gets to meet him. Fred tells him that the gang has also been into some terrifying experiences, Spartan immediately invites them to have dinner at his place, where he promises to show them his latest trophy, the cursed Shrunken Head of Squar Gringot. But when its headless body appears and threatens to pursue the professor until the end of his days for plundering its tomb, the gang must find out a way to break the curse.

When Fred's dad is being attacked by an unknown shadowy figure it's up to Scooby and the gang to get to the bottom of the mystery. Will they be able to, or will Fred have to give up mystery solving forever? And what does the puzzle piece Fred's dad possesses have to do with it all?

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?