The novel is divided into three main sections or books. In the first book, "Recalled to Life," Jarvis Lorry, a London bank manager, accompanies Lucie Manette to Paris to retrieve her father, Doctor Alexandre Manette, who was recently released from prison after 18 years.

Dr. Manette stays with his former servant, Ernest Defarge, and Defarge's wife, Therese. Dr. Manette has lost his sanity in prison and spends his time in a little room making shoes. Lucie reunites with him and brings him to England.

This part of the novel is rich in metaphors and foreshadowing, hinting at the suffering of France's peasants and the impending revolution. For instance, a cask of wine resembling blood bursts open in the street and is eagerly consumed by a hungry mob.

Book the Second, "The Golden Thread," occurs five years later in 1780. Dr. Manette is recovering with the help of Lucie. Charles Darnay, a French immigrant, is on trial for treason. The trial takes a surprising turn when Sydney Carton, a depressed and alcoholic lawyer who looks just like Darnay, creates doubt concerning the witness identifications, leading to Darnay's acquittal.

Four months later, the Manettes lead a peaceful life while Darnay and Carton compete for Lucie's affection. Meanwhile, in Paris, the aristocrats are depicted as gluttonous and callous parasites robbing France of its wealth.

Monseigneur could swallow a great many things with ease and was by some few sullen minds supposed to be rather rapidly swallowing France. (Book 2, Chapter 7)

One aristocrat, the Marquis St. Evrémonde, runs over a child after telling his coachman to drive too fast. At his home, the marquis meets Darnay, his nephew. Disgusted with the cold-heartedness and decadence of the aristocracy, Darney renounces his inheritance and returns to England. Despite their many differences and his lingering love of Lucie, Carton befriends Darnay. Darnay marries Lucie, and they have a child together.

In July 1789, Paris erupts in violence with the Bastille's storming. Darnay returns to France, hoping to rescue his uncle's servant and positively impact the growing revolution.

In the third and final book, "The Track of a Storm," Darnay is arrested in France for being an aristocrat. Monsieur Defarge, escorting him to Paris, refuses to help, emphasizing his duty to the revolution. Dr. Manette and Lucie come to Paris to aid Darnay.

Despite initial hope, when Darnay wins his case, he's arrested again. An account written by Dr. Manette during his imprisonment reveals the crimes of the St. Evrémondes, leading to Darnay's conviction and death sentence. However, Carton, using his resemblance to Darnay, switches places with him and arranges Darnay's escape.

As Darnay and Lucie head back to London, Carton sacrifices himself at the guillotine, declaring,

It is a far, far better thing that I do, than I have ever done; it is a far, far better rest that I go to, than I have ever known. (Book 3, Chapter 15)