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

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.

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.

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.

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 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?

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 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 ghost of Crystal Cove's most famous sheriff, Death Justice, has come back from his grave to make Sheriff Stone quit his job by trapping Crystal Cove's top criminals. Can Scooby and the gang stop Death Justice before it's too late?

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?

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."

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 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.