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

Strange things continue happening in Crystal Cove, when doorknobs suddenly vanish and a priceless diamond is hidden somewhere. To top it all off, a mysterious Ghost Trucker is also scaring the town.

There's a vampire loose in Crystal Cove, terrorizing the residents and stealing an odd assortment of loot. When the gang does some sniffing around, they discover an unlikely suspect… Daphne's MOTHER. Things are already strained within Mystery Inc., and with this latest blow, the gang is truly torn in half. Girls on one side, boys on the other.

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.

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?

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?

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

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 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.