Doctor Pascal, the title character and protagonist, is a physician in a small French town. He has become independently wealthy by making good investments on the advice of his broker—thus, he is not dependent on a medical practice for his income. He therefore devotes most of his time to his passion: medical and genealogical research.

The novel begins with Pascal in his study (as usual), accompanied by Clotilde, his niece and assistant. Clotilde helps him by copying papers and drawing flowers for illustration in Pascal's planned book. One particular feature of the room that the author describes is a carved, antique, wooden cupboard that holds Pascal's papers. These consist of documents and notes collected over thirty years, all on the subject of heredity.

Martine, Pascal's housekeeper, has worked for him for thirty years. Clotilde has been with them for thirteen years, since she was seven years old; after her mother died, her father felt unable to care properly for her. Martine runs the household efficiently and affectionately. She is very religious, and the fact that Pascal is not is a point of contention; she disapproves of him not attending church (whereas Clotilde always does).

Madame Rougon, Pascal's mother, eventually arrives. She deeply disapproves of her son's research and the potions he concocts in his laboratory. Vocally criticizing him in front of Clotilde, she laments the fact that that he wastes his energy treating the poor rather than rich, who would pay him well for the medicines he invents.

Another point of contention between Pascal and his mother is the cache of papers Pascal has accumulated. Knowing that their family has some scandalous episodes in its past, Madame Rougon would prefer that Pascal not collect information about their relatives and ancestors. She nearly succeeds in removing and destroying some papers, but she is interrupted by Pascal. After she leaves, Pascal lashes out at Clotilde for her treason of turning over the key. Henceforth, he personally holds the keys to the cupboard and his desk, which has one drawer full of money.

A few weeks later, Maxime, Clotilde's brother—who is an irresponsible spendthrift—visits from his home in Paris. He asks Clotilde to come live with him, but she prefers to stay with Pascal. The next major development is the arrival in town of a monk, whose preaching impresses Clotilde. Convinced that Pascal's scientific research is dangerously ungodly, she tries unsuccessfully to convince him to give it up and burn his papers. His mother also continues her campaign to burn the files.

A turning point comes when one of Pascal's patients dies after being injected with his experimental potion. The doctor becomes so distraught that the family fears for his sanity, as there is a family precedent for insanity; his elderly grandmother had been institutionalized after losing her mind.

Another major development is Doctor Ramond's courtship of Clotilde. Doctor Raymond is a young physician and close family friend. After some hesitation, Clotilde agrees to his proposal. Pascal's health is negatively affected by the news, and she spends many days nursing him, treatment that even includes injections from another potion. After he improves, the preparations for the wedding begin. However, Pascal he realizes that he feels sexual desire—not just familial affection—for his niece. A few days later, they discuss the situation and she reveals that she loves him, not Ramond, and will break off the engagement. That night, they consummate their love.

From this point forward, they are lovers, lost in a blissful reverie. Catastrophe soon strikes, however, as it turns out that Pascal's broker has been stealing his money. All of his fortune is now gone, save for the cash in the desk. Maxime and Madame Rougon try to persuade Clotilde to move to Paris, but she refuses to go, until Pascal insists. While she is away, he struggles under immense pressure and suffers from a heart attack. She writes to say that she is pregnant with his child and returning home. Before Clotilde can arrive, however, Pascal dies.

Once he is gone, Madame Rougon and Martine burn his files. The cupboard will now hold baby clothes for Clotilde and Pascal's child.