The player begins the game by taking control of Michaelangelo, who must rescue the other turtles, along with Splinter and April O'Neil. Unlike other games based on the franchise, this is a scrolling action-adventure game reminiscent of the Metroid and the later Castlevania: Symphony of the Night. Each turtle has a different ability which is necessary to finish the game. Michaelangelo can hover using his nunchakus as a helicopter, Leonardo can drill the floor by spinning with his katana, Raphael can hide himself inside his shell to enter passages that are otherwise too small to enter, and Donatello can stick to and climb walls.

The bosses are Scratch, Dirtbag, a Triceraton, Scale Tale, and Shredder (in this game known as Cyber-Shredder).