While watching video tapes of old battles, Raphael sees a mystery person spying on them. An alien warlord named Dregg sends his TechnoGansters to steal all the gold on Earth. The Turtles find them attacking the Federal Reserve Building and are outmatched, until a mystery person arrives. Back at the Lair, Donatello announces that the mutagen is unstable and will cause unknown effects on them. They then find the mystery person in the sewers and he reveals himself to be Carter, who in search of Splinter. Meanwhile at the Copcor Building, April sees the unveiling of the new robotic law enforcement: the Intimidators.

Hi-tech is leading a group of technogangsters on a break-in at a Government Lab. The object of their quest? A proton accelerator, but the Turtles and Carter are there waiting for them. The Turtles are ticked off at Carter because, once again, he didn't play like a team member. Carter is angered by their criticism and takes off on his motorcycle. Back at the lair, while Leonardo is unable to locate the Dreggnaught with their tracking equipment, Donatello continues to express concern about the results of his testing of the unstable mutagen. Out of the blue, April contacts them 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, a device that will take pollution down to zero.

Dregg hires an alien bounty hunter named Medusa to help capture the Turtles. The Turtles must fight off this new threat. Meanwhile, Carter realises that he is more of a hindrance than a help. Meanwhile, an alien slug, called a Slorr, hatches & begins terrorising the city.

The Turtles set out to prove Dregg's true motives, after nearly getting arrested by military police at Hyper Dyne Labs. The Techno Gang steal a substance called X-Fire, a highly explosive fuel. The Turtles are also still coming to grips with their unstable mutations.

Using a Hypno Transmitter, Dregg is disrupting all the TV stations in the city with a hypnotic signal, which becomes permanent after 20 minutes. After the Turtles destroy his transmitter, Dregg decides to replicate the Turtles' mutagen in order to make his Techno Gang invincible.

A new foe appears in the form of the time-obsessed Chronos, who has thrown the city into chaos, due to all clocks malfunctioning. Can the Turtles, April O'Neil & Carter stop him before it is too late?

Dregg plans to build a Star Shield, a device that Dregg claims will protect Earth from hostile alien invaders. Meanwhile, the Turtles, with the help of April & her mini-cam, hope to expose Dregg for the fraud that he is. The Turtles also find out that Dregg has built an android replica of Cater.

An interdimensional being called Doomquest comes to Earth to try to get a powerful crystal from Lord Dregg. The turtles find that their unstable mutations are now starting to cause them to lose their intelligence whenever they mutate into their new forms. In the end, April is able to successfully expose Lord Dregg's true intentions to the world.