After the defeat of their old arch nemesis, The Shredder, the Turtles have grown apart as a family. Struggling to keep them together, their rat sensei, Splinter, becomes worried when strange things begin to brew in New York City.

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. Meanwhile Splinter is coming... to a decision.

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

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.

Welcome to a typically chaotic day in the life of Bunny, as she juggles her fashion designer dreams with her day job as an apartment block superintendent.