Slash, the evil mutant turtle, returns to Earth from outer space with a greatly increased IQ and a raygun that turns humans into turtles. He plans to reign as Turtle Supreme, but he will have to get past the Teenage Mutant Ninja Turtles to do it.

The Turtles try to solve a missing snake mystery, but Leonardo is afraid of snakes. A scientist who had a snake venom lab accident and turned into a snake tries to turn the city into a swamp.