The Nightingale covers five primary periods in the lives of Vianne (Rossignol) Mauriac and Isabelle Rossignol.
When Vianne’s husband, Antoine, is conscripted to fight for France against the attacking Germans, Vianne and their daughter, Sophie, try to continue normal life in Carriveau without him, imagining that he will return soon.
Meanwhile, Isabelle is expelled from a French girls’ school and sent home to her estranged father, Julien, in Paris. Julien reluctantly allows her to stay with him, but he soon changes his mind when the Germans break through the French defensive line and approach Paris. Isabelle evacuates Paris, along with thousands of others, and is separated from her companions in the crowd. She journeys on alone and meets her future lover, Gaëtan, who invites her to go to war with him. Eager to do something meaningful with her life, she agrees. They travel together to Carriveau.
When the crowd of Parisian refugees reaches Carriveau, Vianne locks her house because she cannot help them all. As a result, Isabelle and Gaëtan find themselves locked out and sleep in Vianne’s yard. Deciding that Isabelle is not ready for war, Gaëtan leaves for the war front the next morning without her. Vianne tends to Isabelle, and together they learn that France has surrendered to Germany.
The invading Germans assign a Nazi officer named Beck to live with Vianne. Isabelle, outraged by this arrangement, joins the French resistance movement and begins distributing anti-Nazi pamphlets around Carriveau. Vianne, however, becomes fond of Beck and agrees to give him a list of the Jews and Communists who teach at her school, including her best friend, Rachel. Soon after, Vianne is guilt-stricken when everyone on the list is fired from their teaching jobs.
Isabelle’s resistance colleagues ask her to carry a letter to Paris and to remain there to continue her resistance work. She agrees, taking advantage of her sister’s good relationship with Beck to ask for special papers that give her permission to travel. She isn’t in Paris long before she proposes a plan to guide a group of Allied airmen, whose planes have been shot down, across the border into Spain. She adopts the codename the Nightingale. After a successful first trip, the British government agrees to fund her future excursions, and she begins regularly leading groups of airmen out of France.
Vianne is fired from her teaching job after objecting when another teacher is arrested. With no source of income, she and Sophie spend a cold winter with no food while Beck is away. When he returns, Beck insists on caring for them and feeding them, an offer Vianne guiltily accepts. Meanwhile, Rachel and her children are forced to wear yellow stars designating them as Jews.
Isabelle learns that the Germans are planning to send all foreign-born Jews in France to concentration camps. She hides one family in Paris. In Carriveau, Beck warns Rachel that she should go into hiding for a day. Rachel first tries to flee with her children, but shooting breaks out at the security checkpoint, and her daughter, Sarah, is killed. Rachel and her son, Ari, hide in a concealed cellar under Vianne’s barn for a day; Rachel comes out for a few minutes the following afternoon and is arrested, leaving behind Ari. Vianne changes his name to Daniel, and Beck provides forged identity papers for the boy so that he won’t be identified as Jewish.
When an Allied pilot is shot down over Carriveau, Isabelle rescues the pilot and hides him under Vianne’s barn. While looking for the pilot, Beck finds and shoots Isabelle; Vianne kills Beck to save Isabelle’s life. Gaëtan smuggles the wounded Isabelle to safety, and they finally become lovers after years of desiring each other.
With Beck “missing,” a cruel Nazi commander named Von Richter moves into Vianne’s home. Vianne begins rescuing more Jewish children, forging false identity papers for them and sending them to the local Catholic orphanage so that they are not sent to concentration camps with their parents.
Isabelle, whose success as the Nightingale has infuriated the Nazis, is finally captured along with her friend Micheline Babineau. Not realizing that Isabelle is the Nightingale, the Nazis torture her for information. To rescue her, her father, Julien, claims to be the Nightingale and surrenders himself. He is shot while Isabelle watches. She and Micheline are first sent to one concentration camp, then to another, where they remain until they are rescued at the war’s end.
When a friend of Vianne’s is arrested for aiding the resistance, Von Richter threatens Vianne, and she begs him not to harm her children. Von Richter, realizing that her children are her weakness, rapes her regularly by threatening her children. She becomes pregnant by him. When the German soldiers evacuate and her husband, Antoine, returns home, Vianne lies, saying the child is Antoine’s.
People begin returning from concentration camps, and Vianne tries to learn if Ari’s parents are still alive. They are not, but he has relatives in America who want him to live with them. Vianne begs to keep him, but he is taken away. Isabelle returns home from the concentration camp, sick and near death. Gaëtan visits her one last time before she dies.
A few chapters placed throughout the book are set in 1995, roughly fifty years after the WWII narrative. In these chapters, an unnamed elderly woman (later revealed to be Vianne) who is dying of cancer must finally come to terms with her memories of the past. As her son, Julien, moves her to a retirement community, she receives an invitation to an event in Paris commemorating the resistance work of people like her sister, Isabelle. Although she initially refuses to go, she suddenly changes her mind and books a flight to Paris, calling Julien to tell her where she has gone.
Julien meets her at the airport; refusing to allow her to travel alone, he decides to join her. Together they attend the event in Paris, where Vianne speaks in memory of her sister. She also sees Gaëtan, who has named his daughter Isabelle, and Ari de Champlain, who has been searching for Vianne ever since they were separated at the end of the war. Julien realizes that his mother has been keeping many secrets about the war from him. She agrees to tell him all of the secrets except one (that is, the secret of his biological father’s identity).