Penny Parker invites MacGyver to help check out the manor that she's inherited from her Aunt Betty. On her 25th birthday she inherits the house, and that day is today. She's heard that the house is haunted but MacGyver insists that there is no such thing as the supernatural. They pull into town and go to the local newspaper office. The owner, Sylvia Lang, startles Penny with a Halloween mistake after mistaking her for a trick-or-treater. Sylvia has the keys and tells them that the heat and water are hooked up, but the phones aren't connected yet. She describes Betty as crazy, and talks about how her father was a bootlegger. When her father was killed, Betty was pushed over the edge and stayed shut up in the house for years. Finally she disappeared 30 years ago and nobody has found her. After seven years she was declared dead. Penny asks if Sylvia has heard that the house was haunted and she admits that the place has quite the reputation.
As MacGyver and Penny leave, a man watches them from a nearby alleyway, being careful not to be seen. As two young trick-or-treaters pass, he mutters "Betty" at them and they run in terror.
MacGyver and Penny get to the house and Penny notices an open window up above. She notices something but dismisses it as her imagination. They go inside, MacGyver first, and he assures her there's nothing there. He props the front door open with a chair and goes to unload the jeep as it starts raining. He comes back to the front door but it seemingly closes on its own despite the chair and locks itself. Upstairs, Penny sees a door open and goes to investigate. She gets MacGyver and shows him what she found: a beautifully decorated room that she believes belonged to Aunt Betty. MacGyver notes that there's no dust and someone has apparently been keeping it up. As Penny looks through her aunt's wardrobe, noting the dresses are on the large size, she finds a musical jewelry box that plays a tune she thinks sounds familiar. She drops it and it breaks open, revealing a hidden diary with the title "A Penny for Your Thoughts."
Penny goes out to show MacGyver, who appears to have disappeared. He pops out with a birthday cake as a surprise. Penny blows out the candles and makes a wish, and then shows him the diary. She insists that there's something eerie about the house and MacGyver insists there's no such thing as ghosts. Outside, a lightning bolt strikes the gazebo, shattering it, and the power goes out. They go to see what happened. As Penny looks back at the house, she sees a figure in the upstairs window. She trips backward and stumbles over a skull exposed by the explosion.
Sheriff Howels comes out the next morning and wonders if the skull belonged to an Indian. However, MacGyver points out that it has a gold crown. Penny comes out as Howels and MacGyver secure the burial site. Howels goes to town to notify the state authorities after assuring Penny that it can't be Betty. As he leaves, MacGyver notes that Howels doesn't seem particularly concerned. They're unaware that someone is watching them from an upstairs window.
MacGyver goes through the diary and notices that the handwriting gets increasingly erratic. MacGyver comes up with a way to determine if the skull belongs to Betty and goes to town to get some equipment. Penny insists on staying at the house and exploring on her own. She discovers a painting of Betty with its face cut off. In town, MacGyver does some research at the news office while Sylvia explains that Howels is constantly reminded that he's never been able to solve Betty's disappearance. As MacGyver goes through the newspapers, he discovers that someone has cut out the face of every photo of Betty in the archive papers.
Penny reads through the diary and discovers references to a "monster" that was always watching Betty. The music box starts up and Penny hears a noise in the hallway outside. She goes to investigate and the house starts to shake. Penny screams and the vibrations stop momentarily, but then start up again. She runs outside and sees something stirring underneath the tarp. She goes to investigate and someone sticks the skull out: MacGyver. He's found bones confirming the dead person was a woman. They go inside and MacGyver starts reconstructing the face on the skull using erasers, a wig stand, and putty. As he works, Penny reads from the diary. Betty was worried that some unnamed person was sending her to Dr. Simms, who she described as a butcher. Penny finally goes to sleep.
The next morning, MacGyver dozes off in his chair and the mysterious watcher goes upstairs and enters Betty's room where Penny is sleeping on the bed. The man mutters "Betty" and slips away, leaving flowers on the pillow. Penny wakes up and finds them. She goes to thank wake up MacGyver and thank him, but he tells her he didn't leave the flowers. MacGyver admits there's something weird going on and shows her the reconstructed face: it has a strong familial resemblance to Penny.
MacGyver and Penny show the skull to Howels, who is unimpressed and accuses them of tampering with evidence. Penny mentions the diary and MacGyver mentions the Dr. Simms from the diary. Howels, pouring coffee for them, doesn't remember a Dr. Simms and asks to see the diary. Penny, distracted, goes upstairs to get the diary. Once she's gone, Howels sees the diary on Penny's chair and wonders if she's as crazy as her aunt. Upstairs, Penny plays the music box and begins to drift around, talking about coming home and dropping her coffee cup. As Howels leaves, MacGyver hears the music and then checks the bones. He scrapes one with his knife and gets sparks.
Upstairs, Penny continues to act dreamy and puts on one of Betty's dresses. The mystery man watches from a peephole in the wall as Penny goes to the window. She notices a ring in the windowbox outside and examines it. The man inside opens a secret panel and steps into the room, approaching Penny. He says "Betty" and Penny turns in horror, backing away. She screams and MacGyver comes running. He enters the bedroom but Penny has disappeared. MacGyver notices the spilled cup and discovers traces of a drug in it. He also finds the ring and an inscription inside saying "Forever E.P. and C.H." MacGyver hears a squeaking noise and investigates the closet, finding the hidden panel. A flight of stairs leads downward and MacGyver follows them to a room filled with candles and all the missing pictures of Aunt Betty.
Penny is lying on a bed nearby and wakes up. Confused by the drug, she barely recognizes MacGyver at first. She mentions the monster and the man who has abducted Penny runs in and knocks MacGyver unconscious. He wakes up a few minutes later and the man seemingly comes after him. MacGyver holds him off but Penny stops him and explains the man is Virgil. Virgil knew that Penny was acting strange and brought her downstairs to keep her safe. Looking around, MacGyver realizes that the hidden basement room is where Betty's father ran his bootlegging operation. Virgil has been setting up the still, accounting for all the strange noises and vibrations. Checking the pipes, MacGyver discovers that they are contaminated with lead. All of the moonshine was tainted with lead, which accumulated on her skeleton and caused the sparks. It also affected her brain, causing her insanity. MacGyver realizes that the skeleton's bones were shattered in a fall. They try to get Virgil to explain what happened but Sheriff Howels and Sylvia arrive. Howels explains that Betty called him one night and said Virgil was out of control. Howels arrived just in time to see Virgil throw Betty out the window. Sylvia explains that she promised her father to take care of Virgil, who is her brother.
MacGyver says that Howels has fooled them all: the ring has Howels' initials on it. He figures that the ring fell into the windowbox when Howels pushed Betty out the window 30 years ago. Sylvia knows about Simms: he was caught performing abortions. Remembering the large dresses, Penny figures that Betty was pregnant. Howels couldn't afford the scandal of an insane woman carrying his illegitimate child. Howels continues to blame Virgil, who says that he tried to stop Howels. The sheriff breaks down and admits he killed Betty. He draws a gun and shoots off the valve on the still, and then goes out and locks the door behind him. He turns on the boiler and lets the pressure build up. MacGyver spots lime indicating the wall is partially above the ground. He has Virgil take a piece of pipe and cap it while he builds up more pressure. There's a brass patch on the boiler and MacGyver figures it will rupture first, releasing the steam and firing the pipe through the wall. They escape through the hole.
Outside, Sheriff Howels prepares to escape only to discover that his truck won't start. As he tries to get out, the explosion knocks over the gazebo, crushing Howels beneath a support beam. Penny points out that the beam has "Cliff + Betty" written on it.
Later, Virgil is taken away but MacGyver is sure they won't press charges once Sylvia explains the situation. He insists there's an explanation for everything that happened. However, as they turn toward the house, they hear the music box inside playing by itself.