Honoré and Emily meet a woman with a peculiar timeline on the street in London, and when the disoriented Honoré grabs Emily for support, they timeslip back to the year 1805. They arrive on the estate of Sir Edward Fanshawe, a reclusive genius with a talent for making intricate clockwork automata, including fierce guard dogs and a clockwork woman designed to give him pleasure -- the same woman Honoré and Emily saw in London. When she sees Honoré and Emily, a man and a woman acting as equals, this shakes her view of the world, and for the first time, she begins to imagine life as something other than Sir Edward’s plaything. Torn by conflicting emotions, the clockwork woman helps Honoré and Emily to escape from the paranoid Sir Edward, who believes they are here to steal his secrets.
Emily escapes in a glider, but there is only room for one on board, and Honoré remains on the estate. When recaptured, he flatters Sir Edward on his genius, claiming to be a representative of the US Army’s engineering corps. Sir Edward enthusiastically shows Honoré about his workshop, but when he offers to let Honoré “try out” the clockwork woman himself, Honoré politely turns him down -- and the enraged Sir Edward attacks him. The clockwork woman hits Sir Edward in the head with a spanner, knocking him out and saving Honoré’s life, and, shocked by what she has done, allows Honoré to drag her out of the house with him. They flee from the clockwork guard dogs on a mechanical unicorn, and escape over the wall into the world beyond.
Honoré and the woman are viewed with suspicion when they arrive at the nearby village. As they need money to survive while looking for Emily, the clockwork woman draws on her memories of role-playing with Sir Edward to play the part of a prostitute, seduces a local young man and earns enough money to pay for a room at the inn. When asked her name, she sees a stuffed bird in a cage on the wall of the inn, and takes the name “Dove.” Later, she is proud of what she has done, and doesn’t understand Honoré’s uncomfortable reaction; for his part, he isn’t sure whether to respond to her as a living being or as a machine.
Later, Dove makes a business arrangement with a man named Peter, who offers her fifty pounds if she allows him to make love to her in a moving carriage. However, when she boards the carriage, he ties her up and has the driver take her to London, where he works as a procurer for a brothel. There, Dove is reunited with Emily, whom Peter found lying unconscious after she crashed the glider. In order to save Emily from the brutal “training” that will break her spirit, Dove strikes a deal with the brothel’s madam, Bella, offering to put all her skills to use for Bella’s customers on condition that Emily be allowed to work as her maid. Emily continues to look for a way out of their situation, and though Dove is distressed and frightened by the necessity of thinking for herself, it is becoming clear to her that she was not actually happy or fulfilled while she existed only as Sir Edward’s plaything.
Honoré follows Dove to London, where he is set upon by muggers but rescued by a young MP, Sir Richard Hampden. Sir Richard espouses the sanctity of the home and family values in public to further his career, but visits brothels by night, intending to have his fun while young. He helps Honoré to locate Dove, and together, they rescue both Dove and Emily. Upon returning to Sir Richard’s home, the exhausted Honoré and Emily retire to their guest rooms, but Sir Richard seems to assume that Dove will accompany him to his own bed without asking. For the first time, she is upset by this automatic assumption, and she rejects Sir Richard’s advances. Confused by her own feelings, she confronts Honoré, demanding to know how to make something of her life; however, she realises from his pained response that she too has been treating him like an object, an ideal hero rather than a human. She apologises, and Honoré assures her that she too is human.
Looking for something to do while the others sleep, Dove browses Sir Richard’s library and finds a copy of A Vindication of the Rights of Women by Mary Wollstonecroft. Sir Richard keeps the book for research purposes, but doesn’t believe in its views himself; however, upon reading the book, Dove comes to understand that she will only gain true independence if she wins it for herself. She then hears a commotion from upstairs, and arrives in Sir Richard’s room to find that Sir Edward has tracked him down and shot him out of jealousy. When Sir Edward sees the horrified expression on Dove’s face, he flees; however, Dove finds that some part of her remains subservient to him, and she realises that she must return to Sir Edward’s estate and put to rest the unfinished business between them.
Emily and Honoré return to the estate with Dove, but on their way past the village, they learn that hellhounds have been attacking the town and killing men, women and children. The three friends escape from an angry mob of villagers, but are then stalked by the hellhounds -- Sir Edward’s clockwork attack dogs. They must split up to avoid the hounds, but while Dove manages to escape because of her lack of scent, she realises that her friends will remain in danger unless she returns to the manor house and convinces the automatic housekeeper to call off the dogs. Despite her fear of facing Sir Edward alone, Dove returns to the estate to speak to the housekeeper. However, the housekeeper is still bound by logic and its ingrained obedience to Sir Edward, and refuses to call off the dogs without explicit instructions from its master. Dove must rely upon her newfound ability to reason, and she successfully convinces the housekeeper that, since the dogs have killed innocent villagers, the survivors will take their revenge on Sir Edward unless the dogs are called off. The housekeeper is unable to resolve the conflict between obeying Sir Edward’s instructions and saving his life and shuts down.
Sir Edward investigates the commotion and is delighted to find that his consort has returned to him. He had pursued her to London and killed the man who tried to take her from him, but when he saw her expression he feared that he’d lost her forever. Wracked with despair, he didn’t bother to close the gates behind him when he returned, which is how the attack dogs got out. Finally realising that Sir Edward truly cares for nothing but himself, Dove asks him what her name is, and when he assures her that she doesn’t need one, she announces that she’s leaving him; she is not just his plaything, and staying her will stifle her potential. Stunned, Sir Edward then points out that she’s lost the key that keeps her clockwork wound, but just as it seems that she will have no choice but to remain, she realises that she should have run out of power last night. Since she read Mary Wollstonecroft’s book, she has become self-motivated. She departs, leaving Sir Edward to his despair.
Outside, she is reunited with Emily and Honoré, and learns that the dogs shut down at the same time as the housekeeper. Honoré sees that Dove’s timeline has been restored, and before leaping back to their own time, he and Emily assure Dove that she will achieve great things in her life -- but only when she decides what they are for herself. Dove decides to return to London, become a writer, and work towards a revolution in the affairs of women. She is now her own person, as are all women; one day, the men of the world will understand that they are equals.