Penfold and Danger Mouse are testing the security system at the British Cheese Museum when a temporal glitch strikes and the pair discover the museum's prized pink parmesan has somehow vanished, with a baffled Danger Mouse left cradling the crumbs. There's barely enough time for DM to question what is going on before Danger Hedgehog and Danger Mole arrive on the scene to arrest him.

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.