A female aerobic instructor is possessed by an evil spirit of a fallen ninja when coming to his aid. The spirit seeks revenge on those who killed him and uses the female instructor’s body to carry out his mission. The only way the spirit will leave aerobic instructor’s body is with the help of another ninja.

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.