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 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 (Marcie) 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.

A teenager vandalising a neighborhood is attacked by a creature calling itself "Krampus," leaving his hair snow-white with fear. Three more kids are attacked as the gang meets Mayor Nettles and Sheriff Stone at the roller rink and arcade. Realizing that Krampus attacks "bad kids" such as the aforementioned teenager, the gang turn to the imprisoned Mary-Ann Gleardon for help only to have Krampus attack and kidnap her from prison. In the end, it's revealed that the gang had enrolled the forces of Hot Dog Water, Jason Wyatt, Mary-Ann Gleardon, Ex-Mayor Fred Jones Sr., and Charlie the Robot (from the Haunted Museum exhibition) in an elaborate scheme to steal the original Mystery Incorporated's pieces of the Planispheric Disk. After the gang reassembles the disk, the eyes of the Crystal Coffin glow and it mutters "Nibiru."

Five years ago, a gigantic dragon robot attacks the Quest Industries, then promptly vanishes, leaving the security guard's dog unconscious; Dr. Benton Quest works to revive the dog. In the present day, the same robot attacks the gang at city hall as they begin their investigation into the purpose of the Planispheric Disk; however, the gang is saved by Blue Falcon and Dynomutt, who explain that they have been tracking the robot for years. Velma rudely tells the heroes that Crystal Cove is their turf, and Blue Falcon offers the gang to tag along. Together, they find that Quest Industries has been sold to Destroido. Upon investigation, the dragon-robot attacks, intending to kidnap Dynomutt, only to make off with Scooby-Doo instead. Using a tracking device located on Falcon's belt, the gang and Dynomutt are able to locate Dr. Zin's lair and save their friends.

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 gluttonous monster attacks Francilee Jackson on her cooking show. As the gang attempts to eat dinner together, the restaurant is crashed by Rick Spartan and Cachinga, who are on the hunt for the monster. The monster attacks various locations around Crystal Cove, including various restaurants and the museum where Velma's mom works. Meanwhile, Professor Pericles has gone crazy, leaving Mr. E to attempt to seek the treasure without him. Brad and Judy tell Pericles of E's mutiny, and Pericles uses venom injections to force Mr. E to work for him.

Once the gang returns to Crystal Cove, they find out that everyone in town has disappeared below ground. Later that day, after witnessing Mayor Nettles and Sheriff Stone vanish, the gang goes to Fred's house to discuss the Planispheric Disc, Nibiru, the cursed treasure, and an upcoming planetary alignment. After the interruption of Kriegstaffelbots, the gang sets off beneath Crystal Cove, and discovers everyone in town working for Professor Pericles and the rest of the original Mystery Incorporated. After hearing a conversation between the old Mystery, Inc., the gang is convinced they have gone crazy, and devise a tactical plan to bust everyone out and shut down the operation. Shaggy and Scooby go undercover as Kriegstaffelbots, while Fred and the girls attack in a suited-up Mystery Machine. After the word is spread, Sheriff Stone has everyone rebel against the Kriegstaffelbots and go on a riot.

As the gang follows the original Mystery, Inc. through the caverns, they all approach the first gate to the cursed treasure. Professor Pericles knows the gang has been following them, as he calls them out to bring the Keys in order to open the gates. The gang realizes that the Keys and their scenarios seen in the dream world is how they all apply to the gates and the gates being opened. The gang decides to cooperate, after Pericles reveals that they have Hot Dog Water, and opens the first gate. Thanks to Hot Dog Water, the gang enters the first gate; however, Hot Dog Water is killed by the Kriegstaffelbots nearly straight afterwards. The gang arrives at the second gate, and opens it using the mortar bowl. They enter a mysterious rock dimension, where they are greeted and chased by a Rock Monster. After the monster's failure, the gang comes before the third gate, which is opened using the conquistador's helmet. The gate then releases water trapped behind and turns into a boat, allowing Scooby and the gang to escape and become stranded at sea. After learning that the next gate is below the water, the gang comes upon the final gate, which is opened using the flintlock. The gang enters the dimension, which is teeming with lava, and come upon the crystal sarcophagus and cursed treasure, realizing that they are beneath Crystal Cove. The Evil Entity sealed within tries to manipulate the gang into opening the sarcophagus to free it, but the gang realizes the words the being is speaking aren't true. Suddenly, Pericles and the original Mystery Incorporated arrive and Pericles opens the sarcophagus, releasing the Evil Entity.