The plot kicks off with Leonardo, Raphael, Donatello, and Michelangelo searching for their missing master, Splinter. Their quest quickly escalates, throwing them into a conflict involving the Utroms, the Triceraton Republic, and the Federation. Ultimately, the narrative culminates in the Battle Nexus—a multi-dimensional tournament where the greatest warriors from across space and time compete for glory.

The game follows the second season of the 2003 animated series. It transitions from the gritty streets of New York City into the vast reaches of the D'Honeace Galaxy. The narrative is divided into several acts:

PlayStation 2, GameCube, Xbox, Game Boy Advance