The TARDIS materialises on a beach of glass bordering a sea of acid on an island on the planet Marinus. There the four time travellers discover some transparent submarines, empty save in one case for a rubber suit bearing a small tear through which the acid has apparently seeped and dissolved the wearer. Stalked by the submarines' other rubber-suited occupants, the travellers eventually make their way to a large pyramid they have seen in the distance.

Inside the pyramid they encounter Arbitan (George Coulouris), the keeper of the Conscience of Marinus - a machine designed to eliminate fear and aggression from the minds of the planet's inhabitants. Arbitan explains that four of the five micro-circuit keys required to activate the Conscience have been concealed in different locations around the planet to prevent them from falling into the hands of a creature called Yartek (Stephen Dartnell) and his followers the Voords (Martin Cort, Peter Stenson, Gordon Wales) - the rubber-suited assailants - who have developed a resistance to the machine's influence and plan to turn it to their own evil purposes. The machine has now been modified to overcome the Voords' resistance and Arbitan, by placing an impenetrable force field around the TARDIS, coerces the Doctor and his companions into undertaking the retrieval of the keys. He gives them wristwatch-like travel dials which will transport them instantaneously to each of the keys' locations in turn.

In their quest, the travellers visit such exotic locations as the city of Morphoton, where they almost fall prey to the hypnotic influence of disembodied brains (voiced by Heron Carvic) and join forces with Arbitan's daughter Sabetha (Katharine Schofield) and friend Altos (Robin Phillips); a ruined citadel, home to Arbitan's friend Darrius (Edmund Warwick), which is being overrun by rampaging plant life; a snowy wasteland where the dangers include wolves, an unscrupulous hunter named Vasor (Francis de Wolff) and a group of fearsome Ice Soldiers (Alan James, Anthony Verner, Peter Stenson, Michael Allaby); and Millenius, a city where Ian is falsely accused of murder and learns from prosecutor Tarron (Henley Thomas) that the legal rule is 'guilty until proven innocent'.

Eventually, having found the four keys, and also one fake, the travellers return to the island. In their absence, the Voords have murdered Arbitan and taken control, but Ian tricks Yartek into using the fake key along with three of the real ones and, as a result, the Conscience machine is destroyed - a fact about which the Doctor is not altogether unhappy as he considers that man was not meant to be controlled by machine.

_{Synopsis from Doctor Who: The First Doctor Handbook by David J. Howe, Mark Stammers and Stephen James Walker, reprinted with permission; further reproduction is not permitted. Available from Telos}