The player can play as either Leonardo, Donatello, Michelangelo or Raphael. Each turtle has his own unique set of levels to complete. There is a story mode for one or two players, and there is also a versus mode where two players can fight head to head.

In the versus mode, players can fight as all 4 turtles, Splinter, Casey Jones, Hamato Yoshi, The Turtlebot, Hun, Oroku Saki, and The Shredder. A Challenge mode is unlockable by defeating Oroku Saki with any Turtle in the Story Mode, which needs to be complete to unlock Hamato Yoshi and his dojo.