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.

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.