Um acidente faz um barril radioativo abrir, libertando um monstro de esgoto horrível que envolve suas vítimas em iogurte congelado.

Scooby e a turma são obrigados a passar a noite em uma cidade fantasma, e alguém rouba o motor da Máquina de Mistério.

Um misterioso caminhoneiro fantasma está aterrorizando Baía Cristal. Para completar, todas as maçanetas da cidade desaparecem.

A praia de Baía Cristal é atacada por um homem-siri medonho que tem uma queda por jogadoras de vôlei de praia.

Uma criatura medonha chamada Que Horrífico está transformando as crianças de Baía Cristal em monstros.

Alice May, uma nova aluna da Escola de Baía Cristal, está de olho em Fred. Só tem um problema: ela está morta.

A banda favorita de Velma está na cidade e a turma tem lugares na primeira fila. Infelizmente, um espectro maligno chamado Fantasma também tem.

O Festival dos Cavaleiros Reais chega à Baía Cristal e toda a turma está presente. Infelizmente, um gnomo assustador também está lá, atacando os convidados.

Dois monstros brutais passam a destruir a cidade. E, ao que parece, a Mistério SA também está se despedaçando.

Quando uma horrível fera mecanizada começa a atacar a cidade, tudo aponta para Scooby.

Há uma vampira à solta na cidade, aterrorizando os moradores e roubando diversos itens estranhos.

Os insetos estão tomando conta de Baía Cristal e nem os cidadãos mais importantes estão a salvo dos ataques.

A turma da Mistério SA. foi convidada para competir nas finais anuais juvenis do Clube de Resolução de Mistérios.

Uma gangue de ogros motoqueiros decide passar por Baía Cristal e ninguém fica feliz com isso.

O aventureiro favorito de Fred, Rick Spartan, chegou à cidade para dar aula de biologia na escola.

A cidade tem um novo homem da lei e seu nome é Justiça Morta, um xerife morto-vivo que costumava patrulhar as ruas de Baía Cristal.

A turma do Scooby está a um passo de descobrir o que aconteceu com os membros originais da Mistério SA.

O mistério chega ao fim. A turma do Scooby finalmente descobre o que aconteceu com a Mistério SA. original e por que eles desapareceram.

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.

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.

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.

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 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."

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

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.

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.