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. Meanwhile, Dregg's second-in-command, HiTech, is blasted into space, to be replaced by Dregg's top scientist, Mung, as his new second-in-command.

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.

Lord Dregg teleports Shredder and Krang from Dimension X to the Dreadnaught in order to learn more about the Turtles and Earth's weapons. Meanwhile, after permanently stabilizing his mutation, Carter finally leaves the Turtles and returns to college.

After draining the Turtles' life energy and Krang's intelligence, Dregg plans to fire the Vortex Transporter at the Sun, bringing a piece of the Sun down to Earth. If the people of Earth refuse to surrender, Dregg will cause the Earth to become a second Sun.

After re-energizing the present-day Turtles, the Turtles of the past have only 3 hours to get back to their time, or they will all cease to exist. Meanwhile, during the 15 hours it took to re-energize the Turtles, the remainder of Dregg's invasion fleet has been completed and has been unleashed on the city and now the Turtles and Carter have to stop Dregg, Krang, and Shredder.

Dr. Alvin Huxley has demonstrated his breakthrough invention: The Protein Computer, a computer that thinks as fast as a human mind and can be linked to one. When some gangsters break into the Professor's lecture and try to kidnap him, the Turtles arrive and drive the gangsters away. But these are not ordinary gangsters as their boss is is the Globfather, a large slimy green amoeba in a pinstripe suit and fedora. The Globfather is on Earth and wants to get the protein computer for someone who is willing to pay a lot for it.

Lord Dregg has managed to open a gigantic portal that is large enough to pull the entire Earth into Dimension X. While trying to figure out how to stop it, Leonardo, Donatello and Master Splinter are pulled through the portal, after Dregg turns the portal on them.

Lord Dregg launches a final attack on the Ninja Turtles. The Turtles must travel back to the Technodrome to retrieve Krang's old android body to defeat him.