Shredder creates a retro-mutagen gun that can undo any mutation and dares the Turtles to come get it. As Donatello tries to create a fuel source for the vehicle that The Nutrinos left behind, Splinter and the Turtles eventually make their way to the Technodrome just in time to discover Krang in his new body.

The Turtles take over what's left of Baxter Stockman's equipment, to help them track Shredder and the Technodrome and create the turtle Van. Shredder opens a portal to Dimension X in hopes to obtain new weapons. Instead, The Nutrinos - three teenage hot-rodders, and two of Krang's militant Stone Warriors, General Traag and one soldier, come through.

A scientist named Baxter Stockman has created a robot meant for hunting rats, called Mouser. Shredder mass produces the robot and programs them to hunt the biggest rat in New York - Splinter. Shredder wants Baxter dead because he knows too much. Michaelangelo finds out about Krang.

The Turtles find out about the Technodrome and try to find it. Splinter finds the Technodrome and ends up getting kidnapped by Shredder. When the Turtles find the Technodrome, Shredder tells the Turtles who is responsible for covering them in the ooze that mutated them.

The Turtles meet April O'Neil for the first time. Splinter explains the origins of himself and the Turtles.