Teenage Mutant Ninja Turtles 3: The Manhattan Project is a side scrolling beat 'em up game similar to the previous TMNT title for the NES. The game was developed originally for the NES and is not based on an existed arcade version.
The game begins with the turtles on vacation when they receive a message from the Shredder explaining that he's kidnapped April, turned Manhattan island into a floating city, and challenging them to come stop him.
The game continues to support a 2 player simultaneous mode, and has two options, one in which the players can attack each other, and another which prevents that. The turtles can now also toss enemies by pressing down as they attack, and each turtles has a unique special attack by pressing both a and b together.
The game features 8 levels and bosses which include cartoon characters Dirtbag, Groundchuck, Slash, Leatherhead Krang, Bebop and Rocksteady. As well as the villians from the second live action Teenage Mutant Ninja Turtles Movie Tokka, Rahza, and Super Shredder.