Aboard the Dreggnaught, Dregg and Mung are discussing their next move against the Turtles when Mung informs Dregg that, whilst scouting dimensions, he came across two individuals who claimed they were "old acquaintances of the turtles": Shredder and Krang!
Intrigued by the prospect of using the TMNT's mortal enemies as pawns in his grand scheme, Dregg makes preparations to bring Shredder and Krang back to earth. Meanwhile, Donatello cures Carter of his mutation disease, using the process he used to cure his brothers. Carter, wanting to return to civilization decides the time has come to leave The TMNT and New York behind him, and says goodbye.
Elsewhere, at the power plant, Dregg and Mung activate the Vortex Transporter, which causes a citywide blackout, but in Dregg's eyes, the chaos is all worth the effort, as the transporter succeeds in bringing Shredder and Krang back. But the two villains prove to be as sly as Dregg when they are able to get away from him, proclaiming that they and they alone will dominate the earth. They flee into the city.
Carter, meanwhile, sees the chaos that has gripped the city since the blackout, after saving a cab filled with civilians, he changes his mind about leaving.
The blackout has also caused traffic to grind to a halt, and April isn't happy about it, she thinks things can't get any worse, and then Shredder and Krang hijack her cab, and promptly kidnap her. April is able to contact the Turtles, but Shredder cuts her off, they soon find her cab, but it's empty, Krang and Shredder have decided to proceed on foot.
Mungg is able to locate both the TMNT and their foes and transports all of them back to the Power Plant, where Dregg is preparing to subject them to his greatest, most insidious experiment, Shredder tricks Dregg into thinking he's changed his mind about working with him in conquering earth, and the deception pays off, Shredder and Krang engage in a gun-battle with Dregg's soldiers, the Turtles join in the conflict also, and soon all three parties are fighting one another.
But Dregg uses his micro-bots to turn the tide, and recaptures his foes. He then reveals what he intends to do with them: drain their mental energies and infuse them into his own body, with Shredder and the TMNT's honed battle skills and Krang's superior intelligence, Dregg will become the most omnipotent being in this or any other galaxy!