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Ninja Lotus Blossom's nightmares draw her to a strange artifact in the Turtles' possession. The artifact contains an angry spirit, whose wife's soul is within Lotus.
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.