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 also a versus mode where two players can fight head to head. In the versus mode, players can fight as all four turtles, Splinter, Casey Jones, Hamato Yoshi, the Turtlebot, Hun, Oroku Saki, and Shredder.
A "Challenge" mode is unlocked by defeating Oroku Saki with any Turtle in the Story Mode, which needs to be complete to unlock Hamato Yoshi and his dojo.