During a treacherous desert drive with the Mystery Inc. gang, Shaggy Rogers [Scott Innes] accidentally veers onto government property as a fierce sandstorm rages, and a sudden UFO sighting forces him and Scooby-Doo [Scott Innes] to crash near a quiet town. The others press ahead to seek help, while Shaggy and Scooby stay with the van, the Mystery Machine, hoping for rescue. Soon, the pair are chased by a trio of alien visitors that drive them back toward town. After regrouping at a bustling diner, the group is drawn into a web of local rumors: waitress Dottie [Jennifer Hale] explains that the locals haven’t seen aliens, but they’ve heard strange sounds and seen odd lights at night; Chef Sergio [Neil Ross] reports cattle vanishings that frighten the town; and a patron claims to have alien photos, only to reveal they were paintings—yet the mystery tastes curiously of something bigger. The stranger things get, the more the night feels like it’s hiding something, and the gang contemplates a place to sleep for the night.
That night, Shaggy and Scooby are briefly abducted from the roof by the unseen beings, only to be returned by Crystal [Candi Milo] and her dog Amber [Candi Milo]—a pair who arrive with purpose and a story to tell. Crystal declares herself an undercover government agent tasked with investigating alien activity, and she leads Shaggy to the caves where the first encounter happened. There, the explorers uncover glittering gold deposits, but their joy draws pursuit from both the aliens and a group of military police. Meanwhile, the rest of Mystery Inc. enlist Buck [Neil Ross], a resourceful local mechanic, to repair the Mystery Machine. Buck introduces them to Max [Kevin Michael Richardson], a member of SALF (Search for Alien Lifeforms), who invites the gang to meet the team’s reach and resolve. Laura [Audrey Wasilewski] and Steve [Mark Hamill] join the party, but Velma Dinkley [BJ Ward] grows suspicious after noticing dried mud on the SALF boots, a clue that sends her and the others to a nearby canyon to verify what they suspect. In the canyon, they discover a dry riverbed, mining equipment, and gold tucked away in several caves, where they unexpectedly collide with Shaggy, Scooby, Crystal, and Amber.
The tension escalates as the aliens capture Velma, Fred Jones [Frank Welker], and Daphne Blake [Mary Kay Bergman], while the MPs push the others off a ledge. When the MPs depart, the truth comes to light: the SALF team is the real force behind the operation, having uncovered the cave as part of a 19th-century gold mine on government property. They devised alien disguises and even hired impersonators to keep people away and protect their stake in the treasure. In a dramatic turn, Crystal and Amber reveal their true form to rescue Shaggy, Scooby, and the captured members, then work to subdue the SALF conspirators. They reveal that their earlier appearance was tied to signals from the 1960s used to mask their arrival, and with their goodbyes, they depart back into space. With the conspirators arrested and Buck able to repair the Mystery Machine, Mystery Inc. resumes their journey, a little wiser about the mine and the lengths some will go to for treasure.
