The turtles, Groundchuck and Dirtbag are taken to Shellri-La by an alien "Turtleoid" named Kerma. Kerma seeks help from the turtles to defend his planet from a two-headed dragon named Herman the Horrible.

The turtles unmask the dragon as they prove that the menacing creature is actually operated by two renegade Turtleoid delegates. Kerma return the turtles back to Earth, where they destroy Shredder's new Technodrome Mark II and afterwards defeat Chrome Dome.

Michelangelo's strange dreams lead him to seek out Mondo Gecko, a lizard who was caught in the same ooze as the Turtles. Gecko eventually rebels against his boss, Mr. X, and his bombing campaign.