The action of the story follows Sybil Gerard, a political courtesan and daughter of an executed Luddite leader; Edward "Leviathan" Mallory, a paleontologist and explorer; and Laurence Oliphant, a historical figure who, as is portrayed in the book, was a travel writer whose work was a cover for espionage activities "undertaken in the service of Her Majesty".[2] Linking all their stories is the trail of a mysterious set of reportedly very powerful computer punch cards and the individuals fighting to obtain them.
Many characters come to believe that the punch cards are a gambling "modus", a programme that would allow the user to place consistently winning bets. The last chapter reveals that the punched cards represent a program that proves two theorems, which, in reality, would not be discovered until 1931 by Kurt Gödel. Ada Lovelace delivers a lecture on the subject in France.
Defending the cards, Mallory gathers his brothers and Ebenezer Fraser, a secret police officer, to fight the revolutionary Captain Swing, who leads a London riot during "the Stink", a major episode of pollution in which London swelters under an inversion layer (comparable to the London Smog of December 1952).
After the abortive uprising, Oliphant and Sybil Gerard meet at a cafe in Paris. Oliphant informs her that he is aware of her true identity but will not pursue it. However, he wants information that would compromise her seducer, Charles Egremont MP, now regarded as an obstacle to the strategies and political ambitions of Lords Brunel and Babbage. Sybil has longed for an opportunity for vengeance against Egremont, and the resultant political scandal destroys his parliamentary career and aspirations for a merit lordship. Oliphant also encounters a Manhattan-based group of feminist pantomime artists.
After several vignettes that elaborate on the alternate historical origins of the world of The Difference Engine, Lovelace delivers her lecture on Gödel's Theorem, as its counterpart is known in our world. She is chaperoned by Fraser and castigated by Sybil Gerard, who is still unable to forgive Ada's father, the late Lord Byron, for his role in her own father's death.
At the very end of the novel is a depiction of an alternate 1991 from the vantage point of a computer, which is revealed to be the narrator as it achieves self-awareness.
