Shredder wants to rule Manhattan, so he's saturated the neighborhoods with his henchemen. The heroes in a half-shell must out-ninja Shredder and his thugs before time's up in Times Square! Put your best moves to the test against Bebop, Rocksteady, Triceratons, moussers, foot soldiers, gangs and assorted villains in 15 challenging missions. For the first time ever two turtles can join forces to take on the enemy packed streets as a team. Choose Leonardo, Raphael, Michaelangelo or Donatello to shell out each turtle's unique ninja talents. Time is not on your side. You've got to beat the clock as you round up clues and battle it out in the real time fight sequences.

The game is mainly based on the continuity of the original Mirage comics (the opening cutscene even uses some lines from the first issue regarding the Turtles' battle with the Purple Dragons and Splinter telling the Turtles their origin). The game also has characters and elements from the 80s cartoon (multi-colored bandannas, arm bands, and knee pads, Baxter Stockman appearing as a caucasian blond, Bebop and Rocksteady included as bosses, the Turtles' taste for pizza, and April O'Neil being a news reporter who wears a yellow jumpsuit) and the film series (one of the turtles first words is "pizza", just like in the first film; as opposed to "Splinter" like in the Mirage comics, the design of Splinter, the inclusion of Tatsu as a boss, April O'Neil resembling Paige Turco, who played her cinema counterpart in Teenage Mutant Ninja Turtles II: The Secret of the Ooze and Teenage Mutant Ninja Turtles III, the Turtles' rescue of April from a group of Foot Soldiers is similar to a scene from the first movie. ) Despite being based on the Mirage original comics version, the game is still kid-oriented (e.g., the Shredder is turned over to the NYPD in the ending as opposed to being killed).