The Stooges are private detectives that are hired to track down a kidnapped girl name Mary Bopper (Norma Randall), daughter of George B. Bopper. They decide to trace Bopper back to where she was last seen, which leads them to mad scientist Dr. Jeckyl (Philip Van Zandt) and his assistant, Mr. Hyde (Tom Kennedy). There is also a gorilla kept imprisoned in the house for experimental purposes. The Stooges arrive to rescue the kidnapped girl disguised as door-to-door pie salesmen.
Spooks! was the first of two shorts made by Columbia with the Stooges in 3-D, after the 3-D craze of 1953 began with Bwana Devil. It originally premiered on May 20, 1953 with the Columbia western Fort Ti (also in 3-D).
The Stooges' next short in the series, Pardon My Backfire was their next and final attempt at stereoscopic photography.