Our four turtles stand facing their most formidable foe to date - the Shredder. Battle weary, the turtles cannot stand against the Shredder and manage to slip away getting separated in the process. Can they survive apart? Can they get back together in time to save themselves and face the Shredder?

When Don's examination of some mysterious crystals attracts the attention of a subterranean monster, the Turtles underground exploration unearths a Foot Genetics Lab! A video record of strange experiments reveals more of Shredder's mysterious agenda, but when the mutants attack, the boys better watch out, or it's everybody out of the gene pool!