Case History: The Mystery Machine runs out of gas in the countryside, and the gang are threatened by a farmer who is sick of reporters pestering him—it appears that the neighborhood is being haunted by about a ghostly spacecraft. After getting gas, the gang follow the UFO to an abandoned air field. They discover a generator that has been recently running, then split up to look for clues after they see the ghost craft land on the field. Scooby and Shaggy are the first to see the space ghost, which corners them in the wreck of an old bomber, but they escape after deploying the life raft.

Meanwhile, Freddy, Daphne, and Velma find a machine shop that's sloppy with fresh grease. Before they can look into it further, Freddy is hauled up to the ceiling by a hook. No sooner have they rescued Freddy than the space ghost shows up again and the kids flee. Shaggy and Scooby end up in the base's mess hall, where they find fresh food—and odd thing for a ghost from outer space to keep on hand. Before they can find the others to report the clue, they are chased back by the ghost into the mess hall, where Scooby gets an unexpected bath in the automatic dishwasher.

Freddy and the girls find a newspaper that bears the ghost's glowing fingerprints—why would he be interested in local doings? After another close brush with the ghost, Scooby and Shaggy connect with the others by the motor pool, where they are startled by a jeep that runs itself. The are also surprised when an army of ghosts materializes. Scooby and Shaggy duck into the air field's control tower, where they hit pay dirt: a movie projector and a tape recorder hooked up to the field's loudspeakers. They try to get the attention of the others, but the ghost gets to them first and they must dive out of the tower with a parachute.

On the ground, the gang meets up with the farmer and the local sheriff. The ghost retreats into the base's wind tunnel, where he's is trapped and has his disguise torn off when Freddy turns the machinery on. He's revealed to be one of the locals, Henry Bascombe, who had gotten wind that the Air Force was planning to reopen the air base and would be buying up adjacent land for an expansion; Bascomb was trying to scare his neighbors away so he could buy their land cheap for the resale.

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