A quartet of humanoid turtles, trained by their mentor in ninjitsu, must learn to work together to face the menace of Shredder and the Foot Clan.

The Turtles and the Shredder battle once again, this time for the last cannister of the ooze that created the Turtles, which Shredder wants to create an army of new mutants.

The four turtles travel back in time to the days of the legendary and deadly samurai in ancient Japan, where they train to perfect the art of becoming one. The turtles also assist a small village in an uprising.