While the Turtles work on using fragments of the Vortex Crystal to stabilize their mutations, Lord Dregg plans to use the fragments to create another Vortex Crystal to power his Vortex Transporter.

While Raphael, Michaelangelo, Donatello and Carter work on restoring Leonardo to his regular self, Mung steals all the plutonium from a power plant in order for Dregg to build a Plutonium Ray to turn Leonardo into a radioactive killer.

The Turtles', Shredder's and Krang's battles skills, powers, and memories are absorbed into Dregg.

Dregg and his crew plan an invasion Earth to make it his new home base, but first he has to get his transporter chip back from Shredder.

Dr. Alvin Huxley has demonstrated his breakthrough invention: a computer that thinks as fast as a human mind. The Globfather is on Earth and wants to get the protein computer for someone who is willing to pay a lot for it.

With the city breaking apart, the Turtles head to the street to investigate and see the Dreggnaut appear in the sky. With Mung's help, Dregg reprograms the transporter to open a warp in space.

Lord Dregg launches a final attack on the Ninja Turtles.