Donatello invents a machine that can freeze time, which a deranged professor steals as part of a plan to conquer the world.

Dr. Polidorius, a mad scientist plotting to mutate all humanity into aquatic-beings, creates Ray (not the similarly-named Mighty Mutanimals character), who possesses several abilities of different marine species. Ray kidnaps April O'Neil, and Polidorius mutates her into a fish-woman to be Ray's mate.