The Doctor and Rose visit London in October 1924 to attend the British Empire Exhibition. The TARDIS materialises in a scrapyard across the street from Sir George Harding’s home, and when Sir George’s butler, Peter Dickson, investigates the sound, he is attacked by a hulking figure that ticks like a clock. The Doctor and Rose encounter the struggle and intervene, driving off Dickson’s attacker and helping the injured man back home. Sir George and his wife, Lady Anna, are grateful for the strangers’ help, and Harding explains that a number of servants have recently been attacked in the streets. However, when Dickson claims that his attackers questioned him about Harding’s dinner guests, the Doctor realises from Harding’s reaction that he has something particular to hide.
Rose goes upstairs to wash her hands, which she scraped on the road during the struggle, and while trying to find her way back to the stairs, she meets Freddie, Sir George’s stepson. He is up past his bedtime, but is confident that his stepfather won’t thrash him even if he finds out. Freddie offers to show Rose a secret way into the gallery above the library, where they can hide and spy on the dinner guests. Freddie identifies most of the guests, but does not recognise the two men speaking to Sir George and promising to do what they can for “the boy.” Eavesdropping, Rose and Freddie learn that the two strangers are Repple, a nobleman with a curiously fixed expression, and his companion, Major Aske, who constantly stands with his hand in his pocket. Rose notes that Freddie seems tired, and ushers him back to bed, but promises not to tell his parents that he’s been staying up late and spying on them.
The Doctor notes that many of Harding’s guests have Russian names, and gets the impression that they’re waiting for him to leave. He and Rose thus make their farewells and return to the scrapyard, only to find that the TARDIS has been stolen. Reasoning that they’ve attracted the attention of whoever attacked Dickson, the Doctor and Rose thus return to Harding’s to investigate the attack. They arrive just after the final dinner guest: socialite Melissa Heart, who is known as the Painted Lady for her habit of wearing elaborate masks to hide her face. The Doctor leaves his jacket in the library with the other guests’ coats, and explains that he and Rose have been let down and thus have nowhere to stay in London; Repple thus offers to arrange temporary rooms for the Doctor and Rose at his own lodgings, the Imperial Club.
Harding’s guests seem disconcerted by the Doctor’s presence, and are shocked when he simply announces that he’s deduced the real reason for the dinner party: most of the guests are expatriate noble Russians plotting to seize power back from the revolutionaries. They will need to return to Russia with a figurehead in order for their counter-revolution to succeed, and the Doctor deduces that one of the dinner guests must therefore be the heir to the Russian throne. However, it’s Rose who realises that the heir is Freddie; Lady Anna and her son are the only survivors of the Russian royal family. The Doctor and Rose know that the conspiracy is doomed to fail, but say nothing, deciding to allow the conspirators their dreams. Repple explains that he is the former Elector of Dastaria, a small country on Russia’s border; he too has been driven from his home by a coup, and he has offered to help Freddie reclaim his throne in exchange for the Russians helping him to reclaim his own.
As the guests file out of the library and go their separate ways, Rose spots Freddie watching them from the balcony. Melissa Heart is the last to leave, and Aske draws Harding aside for a private word while Repple is speaking with another guest. Meanwhile, the Doctor questions Dickson about his attacker, but Dickson can remember little of significance, except that he heard a strange ticking sound when attacked. As Repple and Aske approach the Doctor to show him to the Imperial Club, Dickson hears the ticking again, but is unable to locate its source. The Doctor then discovers that his jacket has gone missing, along with the sonic screwdriver in its pocket. Unable to locate it, he has little choice but to leave the search to Dickson and set off for the Imperial Club. On the way, Repple and Aske explain that the Club was established by a man named Pooter as a refuge for the dispossessed nobles of Europe; in Pooter’s absence, it is run by its permanent resident, Lord Wyse.
The Doctor and Rose find Wyse playing chess against himself in the panelled Bastille Room while a black cat with a triangle of white fur on its head watches from the settee. As Wyse shows Repple to bed, Aske speaks privately with the Doctor and Rose, claiming that Repple is in fact an actor who suffered a concussion and now believes himself to be the fictional character he was playing at the time; unable to talk his friend out of his delusion, Aske is playing along with it so as to care for him. Crowther the butler shows the Doctor and Rose to their rooms, where Repple contacts them, claiming to have a great secret. As he speaks, there is a sound like a floorboard creaking outside the door, but Repple doesn’t seem to notice, and tells the Doctor and Rose that Aske is really his jailer, a revolutionary agent who keeps his hand in his pocket so that he will be able to draw his weapon at a moment’s notice. The Doctor asks Repple to describe the flag of Dastaria, hoping to catch him out, but Repple describes it without hesitation as a white triangle on a field of black. After Repple has gone, however, the Doctor points out to Rose that the cat is in the room with them, and that Repple just described the pattern on its fur.
Rose retires for the night, and is woken the next morning by the 19-year-old maid, Beth. Rose strikes up a friendly conversation with the shy girl, who reminds her of Gwyneth, and then descends to the Bastille Room for breakfast. There, the Doctor has just won a chess match against Wyse, but he suspects that Wyse deliberately lost the game, which is more difficult than it appears. He asks Wyse about Repple and Aske, and Wyse claims that Aske is really the delusional one; he believes himself to be a great psychiatrist, and Repple is the one who’s playing along with his friend. Presumably when the board creaked outside their room, Repple believed that Aske was listening to him and thus changed his story. Melissa Heart then arrives at the Club to see the Doctor, and invites him and Rose to visit her at her home on Veracity Avenue when they get the chance. She also returns the Doctor’s coat, claiming that she stopped by the Hardings’ and picked it up for him. The contents of its pockets are still in place, but Melissa hesitates when the Doctor offers to stop by the Hardings’ himself and thank them, confirming his suspicion that Melissa is lying about having retrieved his coat from Dickson.
Melissa is in fact hunting someone in particular, and although she’s coming to suspect that the Doctor is the man she’s looking for, the evidence is still circumstantial. Rose had mentioned speaking to Beth earlier, and Melissa thus sends her clockwork companion to question Beth further about the new arrivals; unfortunately, the clockwork figure throttles Beth to death while trying to force answers out of her. Wyse finds the body while strolling around the streets with his cat, and the Doctor, outraged by the innocent girl’s death, vows to stop whatever’s happening. First, however, he plans to clear his head by attending the British Exhibition as he’d originally planned. On the way to the Exhibition, the Doctor and Rose stop off at the Hardings’, but Lady Anna is unable to tell them whether or not Melissa did stop by. Rose meets Freddie again, and learns that he continued to eavesdrop on the grown-ups’ conversation last night and learned that he is the heir to the Russian throne. Realising that Freddie doesn’t get out often, Rose asks Lady Anna if he can accompany them, but Lady Anna refuses, claiming that it’s too dangerous. However, she does ask Dickson to drive the Doctor and Rose to the Exhibition, and allows Freddie to accompany them on the car ride. The Doctor promises to visit Freddie the next day and tell him all about the Exhibition, and as he and Rose tour the Exhibition, they discuss the Russian royal family; Rose knows little about them, apart from their hereditary haemophilia and the fact that they were supposedly all killed during the revolution.
Having enjoyed their visit, the Doctor and Rose return to the Imperial Club, refreshed and capable of focussing their attention on the mysterious attacks and the theft of the TARDIS. While Rose tries to get a good night’s sleep, the Doctor plays chess and discusses politics with Wyse; Wyse disapproves of the Commonwealth and the government’s attitude that an Empire is no longer something to be proud of. Meanwhile, Rose’s sleep is disturbed by the sound of movement from Mr Pooter’s rooms upstairs, and she rises and goes downstairs, only to stumble across an attempted burglary. Melissa Heart has hired two petty criminals, Matty Black and Ronald Cheshunt, to break into the Club and find out all they can about the Doctor and Rose, but the black cat spots the burglars and attacks them, clawing at Cheshunt’s face and drawing the Doctor and Wyse’s attention. When Rose arrives, the Doctor is distracted long enough for Cheshunt to scoop the cat into a sack and flee with Black. Rose pursues them but is unable to catch up, and sees Cheshunt toss the sack into the Thames, where it sinks without trace. She returns to the Club, where she learns from Crowther that Mr Pooter hasn’t returned after all -- and when she enters the Bastille Room to speak to the Doctor, she sees the cat alive and well and sitting on Wyse’s lap.
The next morning, the Doctor visits Sir George’s, supposedly to tell Freddie about his visit to the Exhibition as promised. In fact, he’s realised that Freddie wanted to tell him something earlier, and Freddie now reveals that, while eavesdropping on the guests the other night, he saw Melissa Heart steal the Doctor’s jacket. The Doctor thanks him, but warns the young boy to leave the investigation to him from now on. Meanwhile, Rose decides to investigate the mysterious Pooter, and climbs out onto the Club’s fire escape to spy on the executives’ meeting. However, she can’t get a good angle from where she’s standing; she can see a man stroking the black cat, but can’t make out his face.
The Doctor decides to confront Melissa directly at her home, guessing that she deliberately let him know where she lived in order to force such a confrontation. When he and Rose arrive, Melissa comments that the Doctor seems to turn up everywhere, like a bad wolf; the proper expression is “like a bad penny,” which indicates that English is not the Painted Lady’s first language. Melissa leads the Doctor and Rose into the drawing room, which has a window view of the Thames and two large suits of armour standing on either side of the fireplace; however, the room does not appear lived-in, as though Melissa has been using an unoccupied house for her own purposes. The Doctor asks her why she hides her face behind a mask, but she in turn accuses him of hiding far more important things about himself. She has been searching London for someone with access to alien technology, someone who is always accompanied by a close companion -- and she now believes that the Doctor is the man that she’s been looking for, the man she has come to London to kill.
The two suits of armour come to life, powered by clockwork, and advance on the Doctor and Rose. The Doctor tries to drive them off with his sonic screwdriver, only to find that Melissa removed its power source before she returned it to him. Fortunately, Freddie slipped away from his home earlier to follow the Doctor, and, having witnessed everything, he opens the window from the outside, despite his fear that he could get a splinter or cut himself. The Doctor and Rose escape through the window, and the Doctor thanks Freddie but insists that he return home to safety. The Doctor and Rose return to the Club, reasoning that Melissa will go there anyway to look for them and that they will at least be able to find allies there. He explains the situation to Wyse, but despite his glossing over the more unbelievable aspects, Wyse apparently doesn’t believe him and, though humouring his visitor, claims to have a prior engagement to play chess with a friend along the Embankment. Most of the other guests and staff flee before the clockwork assassins arrive, leaving the Club with only a handful of defenders: Crowther, Repple and Aske, the florid Wensleydale, and the elderly Ranskill and Coleridge. Aske tries to convince Repple to leave as well, but Repple seems convinced that the killers are really after him, and vows to stay and fight.
Rose goes upstairs to contact Mr Pooter, but the doors to the executive office are locked -- and when she tries to force her way in, a black cat emerges from a small panel in the door and fires laser beams out of its eyes at her. Rose manages to grab the cat and smash it against the wall, thus revealing it to be made of clockwork. As she flees downstairs, an identical cat emerges from Mr Pooter’s rooms, but rather than following her, it follows Wyse out of the Club. Evening has fallen, and as the two clockwork soldiers arrive at the Club and begin to batter down the front door, the Doctor decides it’s too dangerous to fight them with so few people and orders his allies to hide. Repple and Aske accompany him and Rose up to Pooter’s rooms, and when they break in, they find that the room contains an anachronistic CCTV system monitoring the entire club. The computer is embossed with a flag-like symbol, a white triangle on a field of black, and is holding more clockwork cats in its storage panels. Rose hears a ticking sound from somewhere, but the Doctor points out that the computer is not made of clockwork; the room is shielded with lead, presumably to prevent anyone from detecting the computer’s energy source, and the mobile units were constructed from clockwork so they could move freely outside the room without being detected.
The Doctor pries a power cable free from the computer and uses it to drive back the clockwork soldiers when they arrive, but then Melissa arrives with a hostage: Freddie, who followed the Doctor and Rose to the club only to be captured by Melissa outside. Melissa threatens to kill the boy unless the Doctor surrenders, and although Aske is willing to call her bluff, the Doctor drops the cable. Melissa reveals that she attended Sir George’s party to investigate rumours that he and his allies intended to restore a deposed ruler to his throne; however, it turned out that they were talking about Freddie, not the man Melissa has been looking for. The triangle flag on the computer, the symbol of the planet Katuria, proves to her satisfaction that she’s found her target at last. Melissa destroys the computer with a laser in her cigarette holder so that it will be unable to stop her from taking the Doctor away to face punishment for his crimes; she believes him to be the war criminal Shade Vassily, who should have been executed rather than exiled.
To Melissa’s surprise, Repple then steps forward and reveals that he is the real Shade Vassily. Aske tries to explain that his friend suffers from delusions, but while Melissa is caught off guard, he pulls his hand out of his pocket to reveal that he’s holding a laser weapon as well. Before he can shoot Melissa, however, one of the Mechanicals puts a blade through his throat; Melissa armed them after the Doctor and Rose escaped from her house. As Repple grieves for his jailer's death, the Doctor wonders why Melissa doesn’t know what her mortal enemy looks like, and Repple explains that he and Aske were given cosmetic surgery so that they would appear human. Melissa removes her mask to reveal her true features; she underwent the same surgery so that she could follow Vassily to Earth, but her intelligence about human physiognomy was flawed, and beneath the mask she appears grotesquely disfigured.
While Melissa is distracted, Crowther and Wensleydale creep up behind her, both having decided that they can’t hide away and do nothing while their friends are in danger. Wensleydale puts a gun to Melissa’s head and forces her to let the others go, but once Freddie and Rose are clear of the room, Wensleydale drops his guard for a moment -- and Melissa shoots him with her “cigarette holder.” The Doctor orders Rose to flee and find Wyse. One of the Mechanicals pursues Rose, Freddie, and Crowther, but Ranskill and Coleridge are waiting on the lower floors in hiding, and they hit the Mechanical with a plank of wood, stunning it just long enough for its targets to get to the fire escape and flee.
Melissa and the Mechanicals take Repple and the Doctor back to her “house,” as Melissa intends to take the Doctor back to Katuria as well to face charges as Vassily’s accomplice. While she prepares to leave, the Doctor and Repple are locked up in a glass tube connecting the “house” to Melissa’s ship, which is hidden beneath the Thames. The Doctor takes the opportunity to question Repple, who explains that Aske convinced him to tone down his true story so that the people of Earth would not think him mad; however, he insists that he was a benevolent dictator and that Melissa’s claims are just propaganda, spread by selfish rebels who just wanted to seize power for themselves. The Doctor notes that Repple grieved for his jailer’s death and was willing to surrender himself to save the lives of innocents; these are not the actions of a selfish tyrant. On the other hand, Melissa’s passionate hatred of Vassily and her willingness to kill innocents for her cause suggest that she truly believes that her actions are justified. Also, the Doctor now realises that he’s heard clockwork ticking whenever Repple was present -- and he now reaches out and pulls off Repple’s face mask to reveal that he too is a complex clockwork automaton, not the real Shade Vassily after all.
Repple is shocked by this revelation, but the Doctor doesn’t have time for him to come to terms with his true nature; instead, he hits Repple’s clockwork head against the side of the tube, weakening the glass, and then kicks the weak spot until it shatters. The Thames floods into the tube, smashing through the airlock’s outer doors and sweeping the Doctor and Repple back into the house. The Doctor nearly drowns, but Repple saves his life. Melissa catches them before they can escape, but Repple shows her his true face, and the Doctor reveals to the stunned Melissa that Repple and Aske were unwitting decoys planted on Earth to lure assassins such as her out into the open. Unfortunately, that plan didn’t take into account the possibility that Melissa might destroy the computer at the club -- and it was the only thing holding the real Shade Vassily in check. Repple explains that his ship’s engines were powered down to prevent him from escaping; the real Vassily will have to use a process of hydrogen extraction to recharge them. The Doctor concludes that Vassily’s ship, like Melissa’s, must be hidden under the Thames -- which means that he’ll probably try to get the power he needs by energising the river’s hydrogen molecules, and the ozone fallout caused as a side-effect will incinerate the entire city of London.
Rose, Crowther, Ranskill and Coleridge take Freddie back home, and Rose then sets off to find Wyse, unaware that Freddie has slipped out of the house to follow her. Wensleydale had claimed earlier that Wyse plays chess with a man named Ben on the Embankment, and as Rose searches the streets, she spots a damaged cat limping towards Parliament’s Clock Tower -- Big Ben. Wyse is indeed there, and when Rose follows the cat into the Tower, he picks up the cat, smashes it against the wall, throws it outside and locks Rose inside the Tower with him. Wyse is the real Shade Vassily, and over the past few months he’s arranged with the Clerk of Works to add extra machinery to Big Ben, claiming that it’s a device that will ensure the clock’s accuracy. In fact, it is storing up energy from the winding clockwork, and when Big Ben strikes the hour, it will release that energy into the Thames, powering up Wyse’s ship. Since the device did not pose an immediate threat, the cats allowed him to construct it -- and now that the cats’ controlling mechanism has been destroyed, they will be unable to prevent him from activating it, escaping from Earth and incidentally destroying London in the process.
Melissa and the Mechanicals accompany the Doctor and Repple to the Embankment, where Freddie finds them and tells them what’s happened to Rose. Smashing down the door will attract unwanted police attention, and the only window within reach is too narrow for anyone but Freddie to crawl through. Repple pulls away the wire mesh around the window, and despite his fears, Freddie crawls through -- only to find that the bolts on the other side of the door are stuck solid. The Doctor sends Freddie to keep an eye on Wyse and Rose while he tries to repair the damaged cat, hoping to use its laser-beam eyes to blast open the door. Melissa returns the power source for the Doctor’s sonic screwdriver and dismantles one of her two Mechanicals to provide him with spare parts, and the Doctor thus reactivates the cat and blasts open the door. He, Repple and Melissa rush into the Tower, followed by the remaining Mechanical, which appears to have noted its fellow’s sacrifice. The damaged cat begins to crawl up the stairs after them.
As Freddie climbs the stairs inside the Tower, he discovers, to his horror, that he cut his leg on the mesh while slipping through the window and is now bleeding. He tracks down Rose and tries to rescue her when Wyse is distracted by the sound of the door blasting open; however, he fails, as he is now too weak to run. When the Doctor arrives, Wyse holds both Freddie and Rose at gunpoint to stop the Doctor from interfering, but the Doctor bolts upstairs, planning to stop the clock from striking and activating Wyse’s mechanism. Wyse pursues him after locking Freddie and Rose in the Prisoners’ Room, a chamber once used to imprison recalcitrant MPs. However, Freddie is still bleeding, and Rose remembers that his family suffers from haemophilia. This is why Lady Anna was so careful not to put her son in danger; once he starts bleeding, he doesn’t stop.
Wyse shoots Melissa’s cigarette holder out of her hand, but when he tries to shoot her as well, Repple takes the bullet for her -- and is unharmed, as he is made of clockwork. Wyse chases the Doctor upstairs, and pushes him out through the clock face; however, Repple arrives just in time and pulls the Doctor back inside. The Doctor sends Repple to check on Freddie and Rose, and Repple frees Rose from the Prisoners’ Room. She rushes off to collect the sonic screwdriver so she can cauterise Freddie’s wound, and as Repple ties a tourniquet around Freddie’s leg, the fading boy tells Repple that he’s happy he got a chance to be a hero. Repple, understanding this desire, sets off to the mechanism’s chamber, intending to jam it. However, he can find no way of doing so, and as he watches helplessly, the clock prepares to strike the hour.
Despite the risk that he will be caught up in his own holocaust, Wyse remains in the Tower to ensure that the Doctor and his allies will be unable to stop the mechanism from activating. Up in the belfry, the Doctor holds Wyse back while Melissa uses the sonic screwdriver to disconnect Wyse’s clockwork from the rest of the clock. Rose arrives, but realises that Melissa’s need for the screwdriver is more urgent and must wait for her to finish -- but the clock begins to strike, and Melissa gives Rose the screwdriver, realising that her own task is hopeless but that Rose might still save Freddie. However, Wyse overpowers the Doctor and chases Rose to the mechanism’s chamber, where he knocks the screwdriver out of her hand. It lands in the middle of the gears, and Rose is caught up in the clockwork when she leaps in to retrieve it. She is nearly ground between the gears, but Repple sticks his hand into the cogs, jamming them just long enough for Rose to get to safety. The grinding clockwork begins to drag the rest of Repple’s body into the gears, but the Mechanical rips his arm off at the shoulder, saving him. Having learned something from its fellow’s sacrifice, the Mechanical then sacrifices itself by stepping into the clockwork, jamming it beyond repair.
Meanwhile, Rose returns to the Prisoners’ Room only to find that Wyse has taken Freddie to the belfry, where he threatens to shoot the boy unless the Doctor and Melissa stop interfering with the mechanism. The Mechanical then sacrifices itself to destroy the mechanism, and Rose arrives just in time to knock the gun aside when the enraged Wyse tries to shoot Freddie. Believing that he’s going to die anyway, Freddie pushes Wyse to the edge of one of the clock’s ventilation shafts, but Wyse pushes him aside before Freddie can knock him in. But by this time, the damaged clockwork cat has reached the belfry, and the Doctor kicks it into Wyse’s face. Caught off balance, Wyse falls into the shaft to his death.
Melissa returns to the TARDIS to the Doctor and leaves Earth in peace, accepting that she is responsible for committing terrible crimes herself in her pursuit of Vassily. The Doctor and Rose take Freddie back to his home; he has survived his experiences, just barely, and for the rest of his life he will remember that he was once a hero. Before leaving, the Doctor grafts one of the Mechanicals’ arms onto Repple’s artificial body; he too will remember that he was once a hero, and will remain on Earth to make a new life for himself, along with the sole surviving clockwork cat.