Mayor Nettles wants the gang to investigate a house that's presumably haunted, according to some reports of the people in the neighborhood. Once inside, Fred says that once they finish the house's research, they have to relocate the Planispheric Disk. Shaggy and Scooby say they'll do it while the others stay in the house, but then Daphne tells everyone that Fred was the last one who hid the Planishperic disk, and that only him knows where it is. After splitting up to look for clues, Fred goes to the basement. There he finds a mirror, but he notices that his reflection is not normal -- it moves differently. When Fred turns around, his reflection pulls him into the mirror, causing Fred to drop his lantern before he disappears.
Fred finds himself in a destroyed and apocalyptic version of Crystal Cove with skeletons everywhere. Just when he starts to think that everyone else is dead (including the other members of the gang), Fred meets an old version of Daphne. Old Daphne tells him that the cause of Crystal Cove's destruction is the planispheric disk, that sped up time in the town, making everyone age faster and therefore, die faster; and that she is the only survivor of the catastrophe. Old Daphne tells Fred that he needs to find the Planispheric Disk in order to "reverse the process" and save the town.
The other members of the gang realize that the house wasn't haunted, it was a cat that made all the noises that worried the neighbors. Shaggy, Daphne, Velma and Scooby are waiting for Fred outside the house, when Evil Fred shows up. Evil Fred makes them think that he is the real Fred. Riding the Mystery Machine, he takes the gang to an Electronics' store, where he takes a radio and headphones. He tells Shaggy to drive while he sits in the co - driver's seat, making Daphne to ride in the backseats along with Velma and Scooby. The gang starts to suspect about Evil Fred.
Meanwhile, Fred takes Old Daphne to the destroyed "F-F-Fearatorium Food Emporium" to search for the disk there. Evil Fred makes the gang to search for the disk in the real Food Emporium. Then, Fred tells Old Daphne that it wasn't there where he hid it, and takes her to the "Arcane-A-Rama Movieplex". Evil Fred then takes the gang to the real Movieplex. After traveling to a couple of more places, the gang realize that they are with a fake Fred, and that the real Fred must be somewhere else. Fred and Old Daphne are attacked by skeletons, and they get inside the Mystery Machine and flee. But then, Fred takes Old Daphne to the real Steelco Industries, telling her that he knows the truth about her. Fred meets Evil Fred and the gang in there. After a fight between the Freds, real Fred takes the Planispheric Disk.
Evil Fred was Fred's dad, Brad Chiles, and Old Daphne was Fred's mom, Judy Reeves. She had been communicating with her husband through the radio, telling him where Fred thought that was the Planispheric Disk. Fred and Judy had been traveling in the abandoned Crystal Cove's movie studio all along, which had been converted in order to be an exact but destroyed replica of the town. Brad and Judy tells the gang that they went through plastic surgery in order to fake their identities. The skeletons where, in reality, robots (Mister Bones Skelo-Bots).
Unfortunately, Professor Pericles shows up, and threatens to kill Daphne with his robots if Fred doesn't give the disk to him. After giving the disk to Pericles, he releases Daphne and escapes. Pericles then takes the Planispheric Disk to a secret chamber in Destroido Corp. and places it in a special location, causing the room to change; saying "I'm coming for you, master. I'm coming to set you free".