The Turtles, Splinter, Casey and April just barely manage to escape from the explosion that destroys the antique store. They hit the road and hide out at Casey's grandmother's old farmhouse, but Leonardo is badly wounded, drifting in an out of consciousness. As he attempts to recover, the Turtles and Splinter tell tales of Leonardo's early adventures, using the stories to help guide him back to the real world.

The Turtles return to New York (as the title might suggest) with one goal in mind: to destroy the Shredder once and for all.