Shaggy Rogers [Casey Kasem] faces a family mystery when his uncle, Colonel Beauregard, dies and leaves him Beauregard Manor, a sprawling Southern plantation. He, along with Scooby-Doo [Don Messick] and Scrappy-Doo [Don Messick], head to the estate to claim the inheritance. Before they arrive, they cross paths with Sheriff Rufus Buzby [Sorrell Booke], who warns that the place is haunted and urges them to turn back. His caution is cut short when a dispatch call arrives about a circus train derailment and a gorilla on the loose, setting a strange, ominous tone for what’s to come.
On the way, their road becomes increasingly eerie, winding through the family cemetery where they confront a Headless Horseman, a ghostly wolf, and the rumored ghost of the Colonel who orders them to leave. When they finally reach Beauregard Manor, they meet Farquard [Arte Johnson], the Colonel’s unnervingly loyal servant, who insists that a vast fortune in jewels lies somewhere on the property and that Shaggy has no rightful claim. Although Shaggy balks at staying, a sudden crash of luck—or bad luck—strikes: their truck sinks into quicksand, trapping them for the night amid a chorus of haunting sights.
To cope with the supernatural chaos, Scrappy-Doo suggests calling in a group of ghost exterminators—the Boo Brothers [Meako, Freako, and Shreako], three specters styled after The Three Stooges. Their efforts are comic and chaotic at best as they try to root out the hauntings. Alongside the trio, Shaggy meets Sadie Mae Scroggins [Victoria Carroll], a shotgun-toting aunt-figure to a feud-filled family, and her brother Billy Bob Scroggins [William Callaway], who is quick to threaten Shaggy. The two families’ long-standing feud with the Beauregard name spices the tension, especially as Sadie develops Affection for Shaggy while Billy Bob’s distrust deepens the danger.
Inside the mansion, the mystery thickens when the kitchen yields proof of the jewel treasure—a diamond ring and a letter from the late Colonel with a clue to follow. The discovery propels a treasure hunt that takes the trio through multiple rooms and hidden corners of the plantation, all while a parade of ghostly visitors intensifies the suspense: the Colonel’s ghost, the Headless Horseman, and a sinister Skull Ghost. Adding to the pressure, they must dodge Billy Bob and Sadie Mae’s ongoing pursuit, fend off a stray bear, and contend with the Boo Brothers’ bungling attempts to help, which only stoke the chaos further.
Amidst the clues, the lost truck reappears, having slipped into an underground tunnel, offering a tangible link to the real world beneath the mansion. The final clue points to a treasure hidden in the fireplace, and the Skull Ghost seizes the moment to threaten the group with a gun as gold begins to pour from the fireplace. The trio unmasked the Skull Ghost only to reveal that the Ghost was one of Sheriff Rufus Buzby’s impersonators, and that the real sheriff arrives to expose that the Skull Ghost was actually his greedy brother, with the remaining specters revealed to be part of the same scheme.
With the treasure secured, Shaggy is convinced by the Boo Brothers that the haunted mansion deserves a new purpose. He donates Beauregard Manor and the jewelry to the Beauregard Trust Fund for Orphans, ensuring the estate will lend its riches to those in need. The trio bids farewell to the place, driving back home with Scooby-Doo and Scrappy-Doo, their adventure seemingly over—until another appearance by the Colonel Beauregard’s ghost rattles the car and Shaggy realizes the haunting may not be finished after all.