Returning from another mission, the TMNT are shocked to discover their mentor has left the lair, leaving behind only a video taped message. Playing the message, the TMNT are informed by their mentor that he has taught them all he knows, and it is time for him to leave them, and for the green machine to grasp their own destinies and go their OWN separate ways.
The Turtles decide to take this final advice and to split up.. Michaelangelo lands a job as a TV cook, Donatello works in a fix-it shop, Leonardo works at a Fitness Centre, and Raphael sacrifices his self-respect to entertain kids at birthday parties. Back in the sewers, his rodent majesty, the Rat King, decides to take advantage of the Turtle's separation and teams up with his one-time enemy, Leatherhead, to cause some mischief. The two rouges scheme to create an army of Robo Rats and Android Alligators to aid in this endeavour, even though the Turtles have disbanded.
Leatherhead still can't resist the urge to hunt down each of the green machine and extract vengeance on them. Rat King seems to agree, and the two quickly ambush and capture most of the TMNT, all except Leonardo.
Leatherhead intercepts the Turtle leader, and the two fight to the finish. During the struggle Leonardo falls down a sewage drain, Leatherhead presumes him dead.
Whilst looking for Michaelangelo, April stumbles onto the Rat King and Leatherhead's agenda, tailing leatherhead [no pun intended], April arrives at the lair where the remaining Turtles are being held hostage.
She is suddenly discovered, but before she can also be corralled by Rat King and Leatherhead, she is quickly rescued by none other than Splinter.
A very much alive Leonardo shows up and quickly frees his brothers, they launch into battle against the shocked villains, after a confrontation with the Android Alligators and Robo Rats. The Turtles force their enemies into retreat. Splinter reveals that his departure was just a ruse to lure Rat King and Leatherhead out of hiding (whilst meditating, he had "sensed" that the two were up to something).