In the distant future, the social outcast Derek Mullard watches a video of the world being destroyed by history's biggest villain - Danger Mouse! To make matters worse, Danger Mouse is Derek's ancient ancestor and the reason he's forbidden from marrying his beautiful paramour, Pennyfold. Meanwhile, in the present day, Danger Mouse is in the midst of foiling Quark's latest plot, which involves auctioning off the nice bits of the world and compact crushing the rest. A time-travelling Derek arrives on the scene to confront Danger Mouse and prevent the world's destruction, correcting the course of history in the process.

On seeing his adopted goldfish get busted for stealing top-secret documents, Penfold bewails the fact he has never had a pet of his own to love and cherish. He gets his wish when Danger Mouse and Squawk discover the Baron's plans to brainwash the world's pets into becoming his personal army of slaves. They hand him the responsibility of babysitting the Baron's own pet Nero, having craftily swapped him with a robotic impersonator as a means of getting to the Baron's mind control device - The Pet Whistle!