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.

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.

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 & Carter stop him before it is too late?

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.

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.

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 try to stop Dregg's Techno Gang from stealing a Proton Accelerator, but due to Carter's interference, the aliens get away. Dregg needs the device to repair his Molecular Converter, but the Turtles need to expose Dregg's true intentions.

A mysterious young man, who has been tracking the Turtles' movements, wishes to train under Master Splinter's guidance. Meanwhile, the Turtles race to stop Lord Dregg's plans for global domination.