Season 2

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 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.

The gang investigate the shocking appearance of a graveyard ghoul who disrupted Shaggy and Scooby's midnight movie.

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.

Snowed in by an avalanche, the gang find themselves trapped in a creepy library.

Deep-sea robots attack Cassidy. The gang helps her solve the case of who is sending them.

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.

An evil goat man named Krampus sends the gang on a quest.

Dr. Zin wreaks havoc on Crystal Cove.

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 monster appears in the middle of Francilee Jackson's cooking show; Dr Rick Spartan helps the gang find out what's going on.

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.

The gang discovers a mirror with a mind of its own.

The group allows themselves to be hypnotized.

The team searches Mayan ruins for the burial chamber of the Hunters of Secrets and the Heart of the Jaguar.

Professor Pericles tries to find the entrance into the caverns where the cursed treasure and the evil entity are buried.

Our heroes travel through the underground caverns.

The heroes must work together to realize that their love for each other is the true Heart of the Jaguar.