Charles Smithson, a member of the English elite, has come to Lyme Regis, a small southwestern town, before his wedding to Ernestina Freeman. Charles is a paleontologist, thirty-two, and a member of the aristocracy. Ernestina is the daughter of a self-made man. Her aunt, Tranter, lives in Lyme and she goes there every year for rest. She has come earlier this year to prepare for her wedding. Charles also arrives, and stays at the White Lion Inn.

Charles learns of the local outcast, Sarah Woodruff, known also as “The French Lieutenant’s Wife” and “Tragedy”. Sarah is employed by Mrs. Poulteney, an elderly widow who has taken her on as a secretary. Mrs. Poulteney is obsessed with her salvation, and with performing acts of good works to ensure it.

Charles and Sarah meet alone accidentally a number of times, and Sarah ultimately reveals her history to Charles. She had hoped to marry a French lieutenant, injured in a shipwreck, who was recovering at the home of the family to whom she was a governess. She gave herself to him sexually, only for him to leave the next day. He later married someone else, and never returned.

Sarah is later fired by Mrs. Poulteney, and she seeks out Charles through a letter. Charles finds her and the two embrace and kiss. Charles, bound by Victorian duty, senses in Sarah possibilities for his own life, and a freedom that he knows will end with marriage. Charles pays for her to leave, to start a new life, and she goes to Exeter near London. Meanwhile, Charles has been disinherited by his uncle, for his uncle intends to marry. Charles then goes to see Ernestina’s father to tell him of the disinheritance. Ernestina’s father offers a larger dowry, and a business position, but Charles declines. John Fowles then presents his first ending: Charles refuses any more contact with Sarah, and marries Ernestina.

In the second and third endings, Charles goes to see Sarah, makes love to her, and calls off his engagement. In the second ending, it is revealed that Sarah, who has disappeared for two years, has had a child by Charles, and a reunion between Sarah and Charles is possible. In the third ending, Sarah rejects Charles, and Charles goes to America.