Somewhere in an alternate Paris, the former Marquis de Sade is feeling hollow, as if something about himself is missing. Sure that something is amiss, he impulsively visits the cells of the New Bastille, where prisoner number six is awaiting execution, his features cloaked by a velvet mask. Unable to find what he is looking for here, Citizen Sade concludes that he is not a man but a monster after all, and retreats to his quarters to indulge himself with a reluctant young guard named Juliette -- who only submits to him out of love for Sade’s adopted son, Minski, the ruler of the new rational France. In his laboratory in the heart of the New Bastille, Minski continues his vile experiments, sewing maggot-viruses into the flesh of an unconscious prostitute and reanimating the decapitated head of a guard whom he had sent into his murder machine for trying to kill him. He continues to resist the entreaties of the forces which he has left behind him, and when they try to communicate with him through the severed head, he sews its mouth shut, first inserting a key for which he has been trying to find a hiding place. He then senses a new arrival in his city, something alien that brings with it the vague sense of British witchcraft. Intrigued, he sends his guards to collect the craft, and to bring its occupants to him...

The Doctor is ailing, his frail body struggling to resist the coming Change he knows will kill a part of him forever. As he fumbles, trying to lock the TARDIS doors, Dodo wanders off to explore her surroundings, and sees the New Bastille towering over Paris -- which she knows to be a historical impossibility. The Doctor finds a poster written in the language of the Revolution but dated to what should be the time of Napoleon, but before he can investigate the discrepancy, the soldiers sent to collect the TARDIS find and arrest him, assuming him to be a curfew breaker. Before Dodo can intervene she is stopped by two actors, Bressac and Dalville, who warn her that it is too dangerous for her to show herself to the soldiers. One of their company, the actress Sophie, has also been arrested by the same patrol; Bressac intends to negotiate for her release tomorrow, and he promises to speak for the Doctor as well. Dodo accepts their hospitality and returns to their caravan, where Dalville tells Bressac that she is too perfect to be true, and that he wishes to corrupt her innocence and despoil her perfect beauty. Bressac knows better; Dalville just wants to sleep with her, and to rationalise his desire he has turned it into a philosophy.

The patrol taking the Doctor and Sophie to the New Bastille is attacked by Garce and Eging, two English spies armed with a weapon supplied by their demonic allies -- a deathmask which burns the French soldiers’ bodies from the inside out. The spies knock the Doctor out, and, leaving him for dead, take Sophie back to their hideout and brutally murder her, using her fear and innocent blood to contact their masters in Hell. The devil Tyll Howlglass appears to them and gives them new instructions; a strange box has recently arrived in Paris, and the occupants may be able to help them. The Doctor arrives too late to save Sophie, but he does meet another young woman -- Catherine Arouette, who helps him to escape from another patrol and promises that they will meet again. The Doctor waits until morning and then visits the New Bastille, claiming to be a regional officer from the southern provinces; however, Minski detects the arrival of an outsider, and sends Sade to investigate. Sade orders Citizen Cameo to throw the Doctor into the unoccupied cell previously inhabited by prisoner 6, and although she seems flustered when she does so, he assumes that this is due to his reputation. In fact, she has fiddled with the paperwork to ensure that her favoured prisoner was not executed -- which means that, unbeknownst to Sade, the Doctor is now sharing a cell with le 6.

While Dodo waits for word of the Doctor, the players’ director, Fantômas, emerges from his caravan to announce that since Sophie has failed to return, Dodo will become the new Sophie. Dodo is reluctant to take on the role, particularly when she reads the play they are to perform. It is The Misfortunes of Virtue by the infamous Marquis de Sade, in which the virtuous lead, Sophie -- who spends much of the play in the nude -- is abused and vilified by evil men, who prosper for their sins while Sophie is struck by lightning and killed. Privately, however, Dodo admits to Dalville that she has been acting all her life, and that much of her shock stems from the fact that Fantômas saw through her mask to the real her. Learning that Bressac is deeply in love with Fantômas, Dodo urges him to tell the director -- but Fantômas rejects him, and when Bressac presses him for an explanation, Fantômas does something to his face which leaves Bressac in a state of shock, unable to comprehend what he has seen. A government official then arrives with a list of changes to be made to the play, in order to make it more palatable for general audiences, and much to Dalville’s shock, Fantômas does not challenge any of the censors’ dictates -- although they are calling for sweeping changes which will alter the entire tone and purpose of the play. Dodo realises that, for some reason, Fantômas is determined to stage the play for Minski, even if the play is changed beyond all recognition.

The Doctor attempts to communicate with his fellow prisoner, who at first appears irrational but is given to bouts of apparent lucidity in which he claims that there are gaps in the air. The Doctor removes the man’s velvet mask, revealing a wary old man who has nearly forgotten how to speak to others. When Cameo tries to stop them from communicating, le 6 overpowers her and escapes with the Doctor, leaving Cameo locked in their cell. As they search for a hiding place, le 6 reveals the sanity behind his apparent madness -- by stepping aside to reveal a hole in the world, through which the Doctor can see the monstrous clockwork of the machine which le 6’s alien contacts have created to operate the world. Meanwhile, the masked masters of Hell prepare for war, and Tyll Howlglass and Larkspur are expelled from the Pageant for suggesting that the system operator seems to welcome their attack. The Pageant, which should have stayed aloof from the world in order to observe the progress of their experiment, is instead becoming a part of it, and is being affected by the system operator’s schemes. Howlglass and Larkspur travel to Paris themselves in search of the new arrivals, in the desperate hope that an outside influence will be able to resist the systems operator and correct the grievous error the Pageant has made. But the others, angered at this betrayal, contact their English allies and order Garce and Eging to kill the renegades.

Prisoner le 6 falls asleep in a sheltered alcove, and the Doctor, sensing a familiar presence in his mind, leaves him to rest while he investigates. The call leads him to Minski’s laboratory, where he finds the TARDIS waiting for him, and meets the still-living severed head. He cuts free the twine from its mouth, and it spits out the key -- but before he can do anything with it he is confronted by Minski himself, the embodiment of cold, heartless rationality in the angelic body of a young child. Minski is aware that the world is a machine, and he seeks total control over the machine and everything in it; to this end, he constructed experimental automata which resembled people, but following his initial experiments he concluded that this was the wrong approach and has rethought his plans. They are now complete, and when the British invade Paris, with the forces of Hell on their side, they will play directly into Minski’s hands.

Investigating reports of an intruder, Sade locates le 6, who flies into a panic upon seeing him and flees after shooting Sade in the shoulder. Unnerved by the encounter, Sade orders his guards to chase le 6 into the murder machine and goes to Minski for advice. Minski leaves the Doctor alone while he deals with the frantic Sade, and the Doctor takes the opportunity to speak with the severed head. It instructs him to use the key to open a portal into the workings of the world-machine; there, he meets an alien named Robin Goodfellow, who has been trapped and enslaved by the process he was supposed to monitor. His people, seeking to understand the human concept of Reason, removed the Earth from the space-time continuum and recreated it within the world-machine, putting in place an organic systems operator derived from the ideals and philosophy of a human from the Age of Reason. The systems operator, however, has expelled the observers from their own experiment, and now seeks total control over the machine and everyone within. The Doctor returns to the laboratory, but before he can even dream up the beginning of a solution, Minski returns and demands that he hand over the TARDIS. As outsiders, the Doctor and the TARDIS have powers beyond those of the world-machine, and Minski seeks those powers for himself. When the Doctor refuses to co-operate, Minski has him sent to the murder machine; he will take what he needs from the Doctor’s friend Dodo.

Dodo observes Fantômas meeting with two hooded figures like monks, but when she eavesdrops on their conversation she realises that the “monks” are aliens, here to discuss the coming war. Larkspur catches her and brings her before Fantômas, who removes his fleshmask disguise to reveal that “he” is in fact Catherine Arouette. Arouette intends to get close enough to Minski to kill him and let the aliens regain control of the world-machine. She has a personal reason for doing so; some time ago, Sade sentenced her brother to death, even though he had pardoned him on the exact same evidence five years before. Knowing that this reality will end when the machine is turned off, Arouette asks Dodo, who is not of this world, to remember them when they are gone. Dodo returns to Dalville and makes love to him, to have something tangible to remember him by -- but Garce and Eging then arrive to execute the disgraced demons and their human ally. Eging uses the deathmask to burn the aliens alive and tries to shoot “Fantômas”, but Bressac throws himself between them and takes the bullet, dying. Garce, driven out of his wits by the screeching of the dying demons, shoots Eging in the head and flees, but Arouette pursues him and uses the deathmask to kill him, wearing her own face as she does so.

The Doctor is reunited with le 6 in the murder machine, a maze of clockwork killing devices and a model of the rational world Minski desires to create; but since this world was constructed from le 6’s ideals, and the machine is a model of the world, le 6 is instinctively in tune with it and can lead the Doctor safely thorugh the traps. He explains that, having seen the spirit of the Revolution swept aside in a tide of bloodlust, he was delighted when the Pageant contacted him and promised to create a world founded on his ideals; but Minski has corrupted that dream. Realising that le 6 is fully attuned to the world-machine, the Doctor has him step through one of the gaps in the world which he showed to the Doctor earlier, and they thus escape from the murder machine and emerge back into the world in the cell area. There, Citizen Cameo -- a true idealist under the guise of a loyal jailer -- helps them to escape to Minski’s private theatre, where no-one will think to look for them. The Doctor leaves le 6 to rest there while he returns to Minski’s laboratory to learn more about his plans.

The players arrive at the New Bastille and are given a sumptuous meal, but Dodo is too upset by Bressac’s death to eat, and Fantômas is also unable to keep anything down. Dodo and Dalville go backstage to rehearse, and are surprised to find le 6 in the dressing room. Believing him to be a fellow actor, Dalville gives him a copy of the play, and he and Dodo make their excuses and leave. At first, le 6 is uninterested -- until he sees the name of the author on the play’s title page, and his memories flood back... Meanwhile, Minski and Sade arrive to greet the players, and Fantômas seems taken aback by the sight of Sade -- who is not at all as he/she expected.

In the laboratory, the traitor’s head reveals to the Doctor that Minski has been sewing up his maggot-viruses in the bodies of prostitutes, and has also perfected another version of the virus which can be spread via food and drink. The city has been besieged by its enemies since the start of Minski’s reign, but by allowing the British to invade the infected city, Minski will ensure that his virus spreads across the entire world. The Doctor analyses the virus further, and finds that it is designed to consume human cerebral and nervous tissue and replace it with a corrupt new form of DNA -- transforming its victims into puppets subject to Minski’s will. Sade arrives and shoots the traitor’s head to prevent it from revealing anything further, and the Doctor, disgusted, tires of looking for the humanity in him. He no longer sees Sade as a man, but a monster -- and he now realises that this is the literal truth. Furious, Sade attacks the Doctor, who defends himself -- and in doing so reveals Sade to be a clockwork automaton. Sade shoots himself in disbelief, and the Doctor sets off to confront Minski, understanding the truth at last.

The allied forces of Britain and Hell descend upon Paris, laying waste to the city, and Minski’s loyal followers, whom he has kept busy with meaningless tasks, are entirely unprepared for the assault. Minski is watching Fantômas’ play when the attack begins, and Arouette disposes of her Fantômas fleshmask and attempts to kill him. However, Minski has already infected her players via the meal they consumed earlier, and at his command they turn on Arouette and prepare to tear her to pieces. Before they can do so, le 6 emerges from backstage and shoots Minski in the chest. The Doctor then arrives, and reveals that le 6 is the real Marquis de Sade; Citizen Sade was an automaton created by Minski, in order to replace the real de Sade with a version Minski could control. Fatally wounded, Minski finds the soldier Juliette whom he had earlier given to Sade, and takes her to the heart of the world-machine, where he orders her to kill herself so he can hibernate within her body until he has healed. Juliette finally sees Minski and her world for what they really are, and she stabs both him and herself to death.

The Doctor and the Marquis de Sade use the key to enter the world-machine, where they fling Minski’s body into the clockwork, bringing the machine to a halt. The Pageant can now rewind Earth’s history back to the point at which they interfered and restore it to its proper place in space and time, and they promise not to conduct any such experiments ever again. The Doctor and Dodo return to the TARDIS and depart, but Dodo does not reveal that she slept with Dalville one last time before the world ended, allowing him to infect her with Minski’s virus. Without Minski it will remain inactive, and she will always have something tangible within her by which to remember Dalville.