Mystery Inc. has disbanded. Crystal Cove is attacked by a Man-Baby called Crybaby Clown. Mayor Nettles is approached by a mysterious figure who gives her the files on Mystery Inc. while stating that she has to get Mystery Inc. back together.

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.

Gary and Ethan are attacked by the Dark Lilith on Mount Diabla and lose the soccer team's lucky soccer ball.

Hebediah Grim, a pilgrim monster is targeting, attacking and judging certain women of Crystal Cove at the lover's hot spot, Lover's Lane.

A family vacationing (the same family which was vacationing in the "The Creeping Creatures") in the Burlington Library is attacked by a wolf creature and scared off. Later, a landslide forces the gang to abandon their ski vacation and detours them to the same library, where they are greeted by its caretaker, Dan Fluunk, who explains to the gang the history behind the mansion, including that its builder and namesake had a fascination with groups of four people and an animal. Soon, strange things begin happening to the gang as their stay in the mansion progresses. Eventually, their experiences are revealed to be hallucinations brought on by burning of a special kind of wood. Meanwhile, Cassidy Williams continues her search for the truth behind why what is happening to the gang now has happened to other gangs in the past -- including the Darrow family.

A robot disguised as a Nazi World War II soldier attacks Cassidy Williams at her radio station, eventually self-destructing as Cassidy fights back, taking the entire building with it. She explains to the gang that these robots have been attacking her for the past week. Robots continue to attack the gang as they investigate. When the gang realizes that the robots are coming from deep underwater, Daphne recruits two of her babysitting charges, Tom and Tub, and their seal (also named Scooby), to transport the gang in their submarine to the robots' spawning vats, in an area the kids call "The Midnight Zone". Shortly after submerging, the sub is attacked by a group of robots and damaged, and the gang stumble upon an underwater base and attempt to use it to repair the sub, only to discover that the base is the factory where the robots are constructed, run by Professor Pericles. In the end, Pericles escapes leaving the laboratory to self-destruct, possibly killing Cassidy Williams as the gang, Tom and Tub, and Scooby the Seal escape.

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.

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

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

A deceased ska band returns from the grave and hypnotizes partygoers at the local nightclub to dance to their music. The gang is called to solve the mystery before they dance themselves to death.

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.

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.

As the gang investigates a haunted house, a man resembling Fred pulls Fred through a mirror and takes him to a world where the Planispheric Disk destroyed all of Crystal Cove. Meanwhile, in the real world, Fred begins acting strangely. The real Fred manages to tell the gang that the Fred in their world is fake, having discovered so when a fake Daphne in the "mirror world" gave herself away. When the ruse is discovered, Professor Pericles uses the Kriegstaffelbots to threaten Daphne in order for the Planispheric Disk to be surrendered to him. When Professor Pericles gets the Planispheric Disk, he makes plans to free his "master.

When a monstrous version of the Freak of Crystal Cove begins appearing in Scooby's nightmares, the gang decides to investigate what's going on. 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. After being hypnotized to enter the dream world, the gang is chased by the Monstrous Freak throughout the dimension. They soon discover the evil entity that was trapped with the cursed treasure, and how previous mystery groups and the people affiliated with the treasure have been manipulated by the entity. The being speaking through Nova tells Mystery Incorporated that they must find the Heart of the Jaguar in order to destroy the evil entity sealed within the crystal sarcophagus.

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.

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.

The gang and original Mystery Incorporated stand before the Evil Entity. The Entity grabs Scooby-Doo, and mentions that he must die and be reborn as a vessel to its darkness. Scooby breaks free, but Pericles volunteers to be possessed by the being, to which the Entity agrees. Professor Pericles believes he has gained ultimate power (due to his growth in size and appearance), but the Evil Entity kills Pericles and mutates his body into a squid-like monster. The Entity then assumes control of the Kriegstaffelbots and summons other evil Anunnaki, who proceed to offer the townspeople for the Entity to consume. When Scooby destroys the sarcophagus, the Entity is killed and a vortex sucks everything in, except for the gang, then explodes. The gang find themselves in a new version of Crystal Cove and Earth itself. After some strange encounters, Mystery Incorporated realizes that all the evil ever caused by the Entity has come undone, thereby changing history.