A small alien being, named Quirx, crash-lands on Earth, with intergalactic stormtroopers in hot pursuit. The Turtles must figure out how to get Quirx back to his home planet, before Earth is destroyed.

Shredder uses a time machine to travel back to Ancient Japan in the year 1583. He plans to defeat Hamato Koji, the man who founded the Foot Clan, and Splinter's great ancestor, for if Hamato Koji is defeated, then Master Splinter would never have been born and the Turtles would forever remain ordinary turtles.