The titular Ark is a giant spaceship carrying Earth's surviving human, plant and animal life in suspended animation en route to a new planet, Refusis II. A few human guardians and their one-eyed, mop-topped servants the Monoids take care of the ship, but when the travellers arrive a plague quickly spreads. Dodo has a cold, and the common cold was wiped out a long time ago and neither human nor Monoid has any resistance. The travellers are placed on trial for deliberately spreading the plague, but the Doctor manages to find a cure and they are allowed to leave...