Krang has created a computer disk holding all available information about Michaelangelo who, at that moment, had eaten every pizza in the lair, forcing Splinter to hypnotize him into craving pizzas no more. Meanwhile, when Shredder attempts to extract information from the disk, there's a malfunction, and Shredder obtains Michaelangelo's personality, while the genuine article is captured by Rocksteady and Bebop.
The Shredder opens a pizza parlor "Weird Pizza" in his latest scheme to catch the turtles. He intends to place a homing device disguised as an anchovy on a pizza, then as soon as the turtles call in with their order and the pizza is delivered, he will send an army of Foot Soldiers into their lair. All he needs is a delivery boy and he ends up hiring the most unlikely candidate: Michaelangelo. This hip turtle is looking for a job so he can buy a new belly board. Not knowing he's really working for Shredder, he jumps into action, and "borrows" the Nutrino Starcruiser. ...
Leatherhead heads to New York to get revenge on the Teenage Mutant Ninja Turtles. He runs into the Rat King instead, who has stolen a truckload of chemicals and plans to turn the citizens of New York into mindless zombies so his minions of rats can rule the city. With two of their most insidious foes in the same sewer, the Ninja Turles must work with April O'Neal to stop them both.