The TARDIS travels to Victorian England on the trail of a time distortion with links to living beings. The Doctor follows a lead to a magician named Octave, who seems to be able to travel between locked cabinets more quickly than humanly possible. Suspecting the truth, the Doctor tries to speak to him after the show, but the terrified Octave drives him away -- and outside, the Doctor meets Sabbath, who is investigating the same problem. Still bitter about the loss of his heart and the way Sabbath manipulated him on Station One and in Spain, the Doctor refuses to discuss the matter with him.
Back in London, the Doctor, Anji and Fitz attend a séance at which a young American, Constance Jane, demonstrates that she has, at least, a genuine ability to read Fitz’s mind; however, the Doctor discovers that part of the performance was faked. Constance seems genuinely distressed by this, and alienist Nathaniel Chiltern theorizes that, rather than being in contact with the spirit world, she suffers from a split personality. He has been attending séances in the hope of finding someone with such a disorder, and he asks Constance to check herself into his clinic for examination. At Chiltern’s request, the Doctor hypnotises her and confirms that she has another personality, a much angrier one who claims that she’s come out more frequently because something is wrong with Time.
Fitz and Anji learn that Nathaniel has had to confine his own twin brother Sebastian in the ward for violent patients. Nathaniel himself suffers from frequent migraines and memory loss, and he frequents opium dens to stave off the pain. He asks the Doctor to hypnotize him in the hope of learning the cause of his trauma, but the Doctor decides to wait until the drugs have worked themselves out of his system. However, back in the clinic, Constance Jane -- or rather, her other personality -- leads him into a trap. Constance has been driven to suicidal despair by the revelation that she has another personality inside her, and in order to stop her from killing herself, the other personality has come out permanently -- and has released Sebastian, who’s managed to explain the truth to her.
The Doctor fears that the time disruptions were caused by a time machine which is currently switched off, and that the consequences could be cataclysmic if it’s switched back on. He thus sets off for Liverpool to confront Octave again. Fitz and Anji visit the Great Exhibition, where Fitz strikes up a friendship with George Williamson, a geologist planning an expedition to Siberia. Rather less friendly is Micah Scale, the owner of a dark room containing a mirror which reflects a rather uninteresting view of a farm. The self-pitying Scale claims that he once had a whole hall of mirrors like this, but that it was stolen from him.
In Liverpool, the Doctor finally contacts Octave and forces him to admit the truth; he is just one man, but in eight bodies. His physical self was splintered by a trip through a mistuned time machine, and he’s barely survived with his sanity intact. The Doctor inquires about the machine, but Octave concludes that the Doctor is more interested in the machine than in helping him, and, enraged, drops a sandbag through the Doctor’s chest, breaking his ribs and crushing his one remaining heart. Impossibly, the Doctor survives these mortal injuries long enough for Anji and Fitz to collect him from hospital and get him back to the TARDIS, where he connects himself to the machines in the sickbay before collapsing into a coma.
While comatose, the Doctor has a vision of a beautiful garden just beyond his grasp; every time he tries to step into it, he is pulled back by a silver thread which pulses like a heartbeat. He awakens in a rage, finally realizing the truth, and sets off to confront Sabbath. It’s easy enough for the Doctor to locate his London dwellings, for he and Sabbath share a link through the same biodata -- since the Doctor’s second heart is now beating in Sabbath’s chest. Already furious, the Doctor is even less impressed to find that Sabbath has recruited the so-called “Angel-Maker,” an Irish girl named Elizabeth Kelly who was found guilty of killing a man and seven children with identical knife blows. In fact, the man had also been splintered in Time; Kelly is time-sensitive, and sensed that the man was wrong in some way. She thus killed him, without realizing that the one blow was striking dead seven other bodies. She is fiercely loyal to the man who rescued her from an asylum and showed her wonders, and when he collapsed at the same time Octave tried to kill the Doctor, it was the Angel-Maker’s frantic beating on his chest which saved his life -- and thus the Doctor’s.
Still upset, the Doctor returns to his rented rooms and finally admits to Anji and Fitz that Sabbath is here. Sabbath’s beliefs about the nature of Time have given the Doctor cause for concern; Sabbath seems to believe that unauthorised time travel causes alternate timelines to proliferate, damaging the structure of the Universe, and the Doctor believes that these views have been cultivated by Sabbath’s mysterious allies? Who are they? And why don’t they want the Doctor dead... yet? The Doctor decides to put these questions aside and investigate the mirror at Scale’s exhibit; it sounds like a camera obscura, a Victorian pinprick camera, but instead of showing what lies outside the caravan it shows something which is nowhere near the Exhibition. Scale reacts violently when the Doctor questions him about his mirrors, but the giant from the freak show, Hugo Little, saves the Doctor from the scuffle. The Doctor rests and recovers in the freak show’s caravan -- where he’s horrified to learn from the freaks that Octave has been murdered.
The Doctor confronts Sabbath once again, realizing that he sent the Angel-Maker to kill Octave. Sabbath had assumed that the fractured humans were the cause of the fracture, but in fact, the Doctor has recognized the symptoms as evidence that someone is experimenting with temporal interferometry. Properly tuned, such a machine breaks apart and reassembles Time as a prism does with light; improperly tuned, it could shatter the fabric of time and space. And since Octave is now dead, they’ve lost their only lead. The Doctor storms off, unaware that Scale had followed him. Scale in fact knows who stole the mirrors from him, and has confronted the thief already; the thief, a gentleman, has paid him handsomely, but Scale has already wasted the money and is still obsessed with the wrong he feels has been done him. Scale tries to break into Sabbath’s house, and although Sabbath questions him he lets him go, deciding that if Scale turns out to be important he’ll lure the Doctor into the thick of things. Meanwhile, while the Doctor is busy, Fitz attends a lecture on Siberia with George Williamson, telling Anji that he’s 33 years old and tired of being a sidekick.
The next day, the Doctor visits Chiltern at the clinic, but Chiltern seems to have undergone a complete change of personality and turns the Doctor away brusquely. The Doctor tries to speak with Chiltern’s brother through his cell window, but the twin appears to be in a state of shock and doesn’t respond to the Doctor’s questions. The Doctor returns to his lodgings, wondering if the twins have changed places, and whether they are also splinters of the same man.
That night, while the Doctor is alone, he is contacted by Micah Scale, who apologises for his earlier behaviour and offers to talk over a drink. The Doctor guesses correctly that Scale has in fact struck a deal with the man who owns the mirrors to turn over the Doctor, who seems to know a lot about them. Hoping to meet the man with the mirrors, the Doctor lets Scale believe that he’s drugged him and allows Scale to lock him in a box in his caravan. He is “rescued” by Hugo Little and Nora the bearded lady, but asks them just to pass on a message to Anji and Fitz while he remains locked up. Nora points out that Scale’s contact might kill Scale rather than pay him, and the Doctor is disturbed to realize that this hadn’t occurred to him. He has Hugo lock him up again, and when Scale returns with transport he tries to warn Scale to run away as soon as he’s delivered him. Scale ignores the warning, and hands the Doctor over to Sebastian Chiltern, who has his orderly, O’Keagh, take Scale away and, presumably, kill him.
The Doctor suspects that the Chiltern “twins” are splinters of the same man, that Nathaniel locked up Sebastian when he tried to explain this, and that learning the truth sent Nathaniel into a state of shock. Sebastian neither confirms nor denies the Doctor’s theory, but drugs him and takes him to the Chiltern family manor on Dartmoor to look at the time machine. There, the Doctor discovers that the framework is designed such that Sebastian never realized a mirror was missing. A brief examination confirms the Doctor’s worst fears; even running tests on the machine could destroy the fabric of the Universe. Sebastian refuses to accept that the machine can’t be fixed, and has the Doctor locked up in an alcove in the wine cellar.
Anji and Fitz receive the Doctor’s note, and reluctantly contact Sabbath to ask for his help. Sabbath claims that he needs access to the technology in the TARDIS to trace the Doctor through their biodata link, but when Anji finally, reluctantly, allows him in, Sabbath finds that the Doctor has set up a force field which prevents him from entering. Sabbath must therefore build his own tracking device, unsure how costly this delay has proven.
In the darkness of the wine cellar, the Doctor is attacked by something that smells of roses and has a prehensile tail which feels like an electrical extension cord. The creature examines him and then retreats. Sebastian is terrified when he learns that it’s free. The Doctor makes one last attempt to convince him that they can work together, but when he refuses once again to repair the machine, Sebastian leaves him locked up and sets off into the darkness with O’Keagh. The creature kills them both and takes the key to the alcove, but the Doctor beats it senseless with the gate and flees out onto the moor. The creature hunts him down, but at the last moment Sabbath arrives in the Jonah and rescues him. Fitz and Anji catch a glimpse of the creature as it retreats; although malformed in some way, it resembled Chiltern.
The Doctor leads Sabbath back to the manor, but the other Chiltern has gone, taking the time machine with him. It seems that Sebastian was also splintered by the mirrors, but if this is the case, where are the other fragments, what’s wrong with the twisted copy, and why didn’t it die when Sebastian did? As they ponder the mysteries, Constance Jane -- or rather, her other personality, “Millie” -- arrives with the dazed Nathaniel. Millie helped Sebastian to escape in order to stop Constance Jane from committing suicide and taking Millie with her, but instead of helping her, Sebastian threw her out and concentrated on helping Nathaniel. Millie blames the Doctor for her troubles, as he was at the séance when it all started to go wrong, and she claims that she could feel herself “falling” towards him and becoming more real.
If Chiltern turns the machine back on it could destroy the Universe, and Nathaniel can’t think of anywhere else it might be hidden. Sabbath believes that this disaster proves that “free will” is a dangerous delusion; when the Doctor disagrees, Sabbath accuses him of endangering the timeline with his recklessness, claiming that whenever the Doctor arrives in a new time period his interference with history creates an alternate timeline, fracturing the Universe and threatening to shatter reality. The Doctor disagrees again, seeing time as a flowing stream; tossing a rock into the stream creates ripples but doesn’t shatter the water. What is Sabbath is wrong, and his drive to “clean up” history results in closing off possibilities, robbing the Universe of choice and depth?
During their argument, Sabbath reminds the Doctor that he owes him his life -- which gives the Doctor an unpleasant idea. The Doctor thus goes out for a walk on the moors, and when Fitz follows him, the Doctor admits that Sabbath is dangerous and must be dealt with permanently. Fitz reluctantly leaves the Doctor to his contemplation, unaware that the Angel-Maker has heard everything -- and when the Angel-Maker stabs him to protect Sabbath, the Doctor ensures that the blow strikes his heart. Fitz and Anji are enraged when the Doctor’s body is found on the moors, but the Angel-Maker doesn’t even notice, as Sabbath has fallen into a coma. As the Angel-Maker holds vigil over Sabbath, Anji watches over the Doctor. Anji doesn’t know why she feels responsible for him, though, and decides that she’s finally had enough; after this is resolved, she will stop travelling with the Doctor.
The Doctor descends into darkness, into a reality deeper than Sabbath can imagine, and speaks respectfully to the dark goddess of these realms. Though contemptuous of the living, she is amused by the Doctor’s cleverness, and when he tells her that this affair will most likely end in a death, she allows him to speak to the shade of Sebastian Chiltern. Sebastian reveals that he and Nathaniel are natural identical twins after all, but that Nathaniel was mad. Feeling responsible for his brother, Sebastian tried to use the time machine to look for a cure in the future, but instead, Nathaniel was splintered. Sebastian tells the Doctor of another family home in Wales, but before the Doctor can learn more about the monstrous other Nathaniel, Death changes her mind and sweeps him away to pay the price for his knowledge. Sabbath arrives in the dark realms, where Death tries to trick him into snapping the thread which links him to the Doctor; however, he still needs the Doctor alive for reasons of his own, and he realizes that she is trying to trick him because she can’t do it herself. Disgusted, she allows Sabbath to take the Doctor out of her sight; however, Sabbath understands what the Doctor has done, and realizes that he can never afford to underestimate him again.
The Doctor and Sabbath return to consciousness, and the Doctor admits to the Angel-Maker that he tricked her, and that he and Sabbath keep each other alive through their shared heart. He then arranges for Nathaniel and Constance Jane to return to London, mainly to get Nathaniel away from Sabbath before Sabbath works out what the Doctor learned and deduces the truth -- as Sebastian wasn’t linked to the other Chiltern after all, but Nathaniel is, killing Nathaniel would kill the other Chiltern, just as killing one Octave killed all the others. The Doctor refuses to let Sabbath consider murdering an innocent, and points out that if Sabbath simply kills Chiltern then they will lose their only lead on the time machine, thus running the risk that someone else will find it and start this all over again.
The Doctor, Sabbath, and their companions travel to Wales, but find no sign of Chiltern or the time machine. While waiting, Sabbath questions the Doctor’s faith that things will turn out for the best, and points out that the Doctor has a history of inexplicable last-minute escapes; guns jam, buildings collapse seconds after he gets out, dictators change their deepest beliefs at the last moment, and so forth. The Doctor, disturbed by the conversation, decides to return to London and see whether the TARDIS can locate the time machine even while deactivated. On the way, he asks Anji what she thinks about his luck, and is disturbed when Anji suggests that he does seem to act as a catalyst in tense situations, tipping latent possibilities one way or the other.
Back in London, the Doctor sets the TARDIS scanning Wales, and leaves Fitz and Anji to keep an eye on it while he tidies up a loose end by fetching the eighth mirror from Scale’s exhibit. However, he finds Chiltern waiting for him there, and this time sees him clearly. Nathaniel has always been mad, but Sebastian just wouldn’t let it lie -- and now he’s become much worse since he was splintered through Time. This fragment managed to pull most of the others back into himself... along with a few other things from the year 1957. There is a toaster growing out of his back, and there is a mouth where his eye should be, a living worm in place of his little finger, and a rosebush in place of his left leg.
Chiltern drags the Doctor to the stage of the Phantasmagorical Exhibit, where Nathaniel has sent Constance through the machine into the past. With the eighth mirror in place she has succeeded in entering her own past and preventing the trauma which caused her personality to splinter, and, luckily, Time has healed itself around this minor change. Nathaniel walks Constance home while the Doctor remains with Chiltern, and the Doctor, understanding the implied threat, lets him go. Chiltern notes that the Doctor seems fearful of entering the machine, and decides to throw him in -- but as the Doctor struggles to escape, Sabbath turns up and advises Chiltern to stop. Sabbath believes that due to the Doctor’s unique relationship with Time, putting him into the machine could destroy it... and that the Doctor is fully aware of this and was trying to trick Chiltern. However, Sabbath wants the time machine for himself.
The Doctor pulls himself free of Chiltern and enters the machine, which shatters around him -- but as the mirrors break, the Doctor sees seven other unfamiliar faces in them. He emerges from the wreckage of the machine to find that Chiltern tried to attack him, but that the Angel-Maker, now knowing that the Doctor’s and Sabbath’s lives were connected, intervened to save his life. Chiltern killed the Angel-Maker, and Sabbath snapped his neck, also killing Nathaniel as he walked Constance Jane home. The Doctor realizes that Sabbath loved the Angel-Maker, in his own way -- and, enraged at this last insult, Sabbath tears the Doctor’s second heart from his chest and departs. The second heart is dead at last, and now the Doctor can grow a new one. The Doctor gives the dead heart to Hugo Little as thanks for his help, and returns to the TARDIS to ponder what Sabbath had said. Is he really an agent for change? Do the laws of probability change in his vicinity?