Rupert Brown (voiced by Eric Taslitz) and Amelia Daley (voiced by Nancy McKeon) are classmates who discover that their teacher, Miss Switch (voiced by Janet Waldo), is a witch with a magical talking cat named Bathsheba (voiced by June Foray).

Miss Switch and Bathsheba fly to Witch Mountain with Rupert and Amelia in their plan to stop the wicked witch Saturna (voiced by June Foray), who has condemned Miss Switch and taken control of the Witches' Council.

Scruffy (voiced by Nancy McKeon) is a lovable puppy struggling to survive in an unfamiliar world where she loses loved ones, battles fiendish foes and learns the value of loyal friends.

Scruffy – frightened and freezing – returns alone to the big city and finds an affectionate new master, a ragged but regal Shakespearean street performer named Tibbles (voiced by Hans Conried).

Scruffy meets a tough bulldog named Butch (voiced by Michael Bell) who takes her to join his family of strays who have set up a canine commune in an abandoned station wagon.