While watching video tapes of old battles, Raphael sees a mystery person spying on them. While the Turtles investigate, an alien warlord named Dregg sends his TechnoGansters to steal all the gold on Earth.

April contacts the Turtles to let them know that Dregg has landed on Earth and is preparing a press conference. The Turtles rush to meet April at the Park, where they hear Dregg announce his friendly intentions and offers the world his molecular converter.

Believing that the Turtles are the only thing that stands between him and total domination of the planet Dregg makes contact with Medusa, a sinisterly beautiful alien.

After challenging Dregg to a final showdown, the Turtles find themselves on the losing end. Only this time, their new mutations have been captured on film and the world believes the Super Turtles to be evil monsters.

April contacts the Turtles to inform them that all the TV stations in the City are jammed. Sleazebug tries to recruit the Turtles for a martial arts tournament.

Carter, April and the Turtles investigate a break-in at the Antique Timepiece Museum. Convinced that Dregg is responsible, the Turtles discover a clue on a wall display.

Splinter convinces the Turtles that it is their duty to fight evil, even when the whole world is against them. Carter and the Turtles team up with April to get the goods on Dregg.

Dregg broadcasts his message to the citizens of Earth about the evil mutant Turtles. The Turtles mutate in broad daylight, attack a squad of Techno Gangsters, scaring the local citizenry.

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.

Mungg informs Dregg that he came across two individuals who claimed they were old acquaintances of the turtles: Shredder and Krang!

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.