In addition to the traditional cases they always solve, the team finds itself being nudged into the uncovering of a dark secret that is hidden in the past of Crystal Cove, covered up by parties unknown.
Meanwhile, while Mayor Jones is running against George Avocados for reelection, Barty and Nan Blake try to set Daphne up with wealthy heir Rung Ladderton.
With Angel's help, the gang finds out that Avocados purchased tires identical to those on the ghost truck, and that his father stole a priceless diamond long ago and hid it as a doorknob.
Suspecting Avocados, the gang traps the ghost truck, only to discover its driver is Rung, who is not as wealthy as the Blakes believed and needs the diamond to restore his fortune.
Villain: The Ghost Truck (driven by Rung Ladderton) A giant crab interrupts a volleyball game at the Crystal Cove beach, taking the players hostage.
Villain: The Phantom/Daniel Frezette (Fantzee Pantz) The gang attends Crystal Cove's Royal Knights Fair, where an evil gnome is paralyzing those dressed as pirates to punish them for their historical inaccuracy.
Velma reveals her relationship with Shaggy, while the gang begins to suspect one of the fair's owners who vocally expresses hate for pirates and is short enough to be the gnome.
Villains: Green Humungonaut and Red Humungonaut/Jax and Max Minner When a violent dog begins terrorizing Crystal Cove, Stone wrongfully arrests and locks up Scooby-Doo.
Villain: Fright Hound/A robotic dog controlled by Mrs. Wyatt While the gang grows more divided, a vampire is stealing seemingly random items from around Crystal Cove.
Overarching Mystery Event: Darrow Family Archives are stolen from the university by Mr. E. Villain: Char Gar Gothakon/Howard E. Roberts A cicada creature is attacking Destroido employees after demanding they quit their jobs.
All the human mystery solvers are taken hostage by Lord Infernicus, while Scooby, Jabberjaw, Speed Buggy, Captain Caveman and J. Wellington "Mudsy" Muddlemore try and stop him.
Villain: Danny Darrow Exchange student Mai Le arrives in Crystal Cove and joins the gang at the Blake mansion for a dinner party with Mr. Wang, a visitor from China.
Mayor Jones buys an ancient Persian temple for Crystal Cove's Creepy Spooky Terror Land, only to find it haunted by a manticore who begins attacking visitors.
The gang traps the manticore, revealing it to be Marcie, aka Hot Dog Water, who wanted the park closed so she could melt down the steel used on the roller coasters and process it into an expensive super helium.
Velma is revealed to have been working with Mr. E. Villain: Baba Yaga/Curator Vronsky Crybaby Clown returns to Crystal Cove to kidnap a therapist, a hairdresser, a plastic surgeon, and a publicist.
The gang invades the dream of the Dreamweaver, revealed to be victim Horbert Feist, who wanted revenge for losing his Crypts and Creatures character years ago.
Villain: Dreamweaver/Horbert Feist Gene Shepherd's Traveling Curio Cabinet of Curiosities brings a Hodag of Horror to Crystal Cove who comes to life and begins stealing from people.
Villain: Hodag of Horror/Roberto the Monkey (under the control of Ned Fussbuster via ringing bells) Modern artist Randy Warsaw presents his latest work of art, "Junk" to Crystal Cove.
In their office, the gang realizes that the gold statues are arranged like the main subjects of a painting, and the music playing whenever Junk attacks is a polka song slowed down.
Villain: Hebediah Grim/Gary and Ethan The gang get stuck in the mountains, and seek lodging at the Burlington Library, where its caretaker Dan Fluunk introduces the mansion's history and the fascination of groups of four mystery solvers and an animal.
Overarching Mystery Events: The lost original settlement of Crystal Cove, which vanished over three centuries ago, now submerged beneath the sea; its inhabitant missionaries were the conquistadors who were the source of Crystal Cove's curse; the base revealed to have been constructed by Frau Abigail Gluck, a member of an old mystery-solving group, the Benevolent Lodge of Mystery; her body whispers "Nibiru" upon its discovery; the final piece of the Planispheric Disk, found by Professor Pericles.
Overarching Mystery Event: Velma finds that the word "Nibiru" refers to an ancient Babylonian prophecy of a collision between Earth and a large planetary object known as "Planet X," whose inhabitants were the first recorded instances of gods.
Villains: Skull Cattle (created by Professor Pericles) Deceased ska band Rude Boy and the Skatastics returns from the grave and hypnotizes partygoers at a local nightclub to dance to their music.
They find that Skipper Shelton's hat (given to him by Handsome Jimmy from "Night on Haunted Mountain") bears the name "S. Llave" written under the brim, which they discover is the second key.
Overarching Mystery Events: Professor Pericles appears to be serving the Evil Entity sealed within the crystal sarcophagus, and has been on a mission to gain access to the Planispheric Disk to set the being free.
They seek the help of the reclusive hypnotist Professor Horatio Kharon (author of the book Velma has been reading), who has also been seeing the Freak within his dreams as well as appearing in Scooby's.
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 forced to work for Professor Pericles and the rest of the original Mystery Incorporated.
Villains: Professor Pericles, Brad Chiles, Judy Reeves, Mr. E, and the Kriegstaffelbots As the gang follows the original Mystery, Inc. through the caverns, they all approach the first gate to the cursed treasure.
Fred uses a trap built into the gate to distract Pericles, and Hot Dog Water captures him to buy the gang time to escape, although she is killed by the Kriegstaffelbots shortly after.