The Ghostbusters race back in time to rescue Futura from Prime Evil at a Salem witch trial. They must not only stop the villain's latest plan, but they must convince the townsfolk that they are not evil spirits.

While patrolling the skies the Ghostbusters are taken by surprise and Tracy is kidnapped. Traveling to another planet the Ghostbusters learn that it is the Great Ghost Gorilla who has kidnapped Tracy and is planning to use him as the model for an army of super gorilla robots.

Prime Evil's rival, Big Evil arrives at Hauntquarters and using his Specter Scepter overpowers and imprisons the villain. In order to save the Earth the Ghostbusters find themselves working alongside Prime Evil.

When Prime Evil sends Fangster to retrieve the Aztec Medallion, the Headless Horseman of Sleepy Hollow, a former hench-ghost of Prime Evil arrives at the Ghostbusters Ghost Command warning them of the danger. But can they trust him?

When Prime Evil's cousin, Count Grumpette creates a double of Tracy using some of the ape's hairs he sends the clone to create havoc. The Ghostbusters are shocked when Tracy is imprisoned and vow to prove their friend's innocence.