Shredder & Krang are still loose on Earth, but without the resources of the Technodrome, they plan to steal equipment from the abandoned Hall of Science at the World Fair. Krang's former weapons engineer, Drakus, using the guise of Beserko, also shows up to cause trouble.

While Krang tries to re-acquire the Technodrome from Dimension X, Shredder tracks down the Rat King & makes an alliance with him in order to destroy the Turtles.

A band of ninja, led by a mysterious villain named Megavolt, are stealing electronic equipment from power plants all over the city, and the Turtles are being blamed for the crimes. The Turtles must find a way to defeat Megavolt & clear their names before it is too late

A mysterious organization of mutants calling itself Highly Advanced Variety Of Creatures has surfaced in the city. Although their pro-mutant intentions seem good on the outside, what are their true motives? The Turtles must find out.

Titanus & his H.A.V.O.C. organization are back, and this time they are planning to build a Sky Platform so that they can retrieve a lost Flux Transformer from a military base. The Turtles rescue a resident of Dimension X, named Gargon, held captive by Krang on Earth, who agrees to help track down Shredder & Krang.

Still after the Flux Transformer, Titanus & his mutants track its unique electronic signals, in order to locate it & get it back. Meanwhile, the Turtles have their hands full, when an enforcer named Krakus shows up. The Turtles must find out who Krakus is & whether he is friend or foe.

Krang & Shredder steal the Astro-Viewer, a powerful telescope, before disabling a starfighter passing over Earth. Once aboard the starfighter, Shredder steals the Fire Star, a crystalline fragment with the power of 1000 suns which renders its possessor invincible.

Krang & Shredder are using the city's power to operate Krang's new Transdimensional Portal to Dimension X, so that they finally has access to their Rock Soldier armies & resources.