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 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.

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.

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.

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?

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 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?

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?

The gang investigates Sheriff Stone's alien abduction claims while real aliens are stealing valuables from Crystal Cove.

A polite Englishman in a mask calling himself the Dandy Highwayman kidnaps several women from around Crystal Cove, including Mayor Nettles, Daphne, and Mrs. Blake.

The gang, accompanied by Velma's mom, goes to Yucatán in an attempt to search for the Heart of the Jaguar after Angie's old friend, Professor Enrique Andelusossa, is "consumed by the jungle" near the Temple of the Hunters (the burial site of the Hunters of Secrets where the Heart of the Jaguar is kept). Upon arriving in Yucatán, the gang visits Professor Enrique's antique shop, where they are greeted by his angry wife, who says Mrs. Dinkley is to blame for his disappearance. After hours, the gang returns to the store, only to be attacked by the Mayan Priestess who warns them away from the temple. The gang ignores her threat and travels into the jungle to find the temple. Due to Fred's master trap skills, Mystery Incorporated overcomes the temple's diabolical traps and discovers the Heart of the Jaguar in the tomb. The Priestess attacks, but fails and is captured by the traps in the temple, which she triggered. Afterwards, a woman who had been spying on the gang appears, but is revealed as working with Mayor Nettles.