The novel begins in August 1944 as Allied forces prepare to bomb the French city of Saint-Malo, which is being held by the Germans. In preparation for the bombing, leaflets instructing citizens to flee are showered down upon the city. Marie-Laure Leblanc, a blind sixteen-year old girl, lives in an ancient house in Saint-Malo. As the start of the bombing approaches, Marie-Laure is home alone, awaiting the return of her great-uncle, Etienne. She occupies herself with an intricate scale model of the city. Meanwhile, in a former hotel in Saint-Malo, an eighteen-year-old German soldier named Werner Pfennig is awakened and ordered to move to the cellar in anticipation of the bombing. The German and Austrian forces are trying to shoot down as many Allied planes as possible. The other residents of the city are unsure what to expect: at this point in the war, the tide has clearly turned against the Germans, but they have a strong and well-fortified foothold in Saint-Malo.
Because Marie-Laure is blind, she cannot read the leaflet warning her. She fiddles with the model of the house where she lives with her uncle and accidentally opens a hidden latch. Some sort of stone falls into her hand. As the bombing begins, Marie-Laure shelters under her bed with the stone clutched in her hands. Meanwhile, Werner is joined in the cellar by Volkheimer, a staff sergeant, and Bernd, an engineer. As the guns continue to fire, Werner thinks about childhood memories and his sister, Jutta.
The narrative shifts to ten years prior, in 1934. Marie-Laure, aged six, lives in Paris with her father. Daniel Leblanc works at the Museum of Natural History. One day, Marie-Laure hears a story about a famous diamond called the Sea of Flames, which is supposedly hidden in a top-secret location in the museum. Legend has it that the Sea of Flames was first found by an ancient prince. After he picked it up, he survived a dangerous attack but began to experience many losses of those he loved. A priest informed him that the stone was cursed: anyone who possesses it will live forever, but everyone the possessor loves will suffer. The only way to lift the curse is to return the diamond to the sea. The stubborn prince, however, refused to do so, and a short time later, the kingdom was attacked, and the stone was lost. Hundreds of years later, a gem trader purchased the Sea of Flames for a French duke. However, the duke suffered so many calamities that he finally donated the diamond to the museum on the condition that it be kept locked up for 200 years. Marie-Laure is doubtful about whether the story is true or merely the stuff of legends.
At about the same time, a young Werner resides in a mining town called Zollverein, in Germany. Werner and his younger sister, Jutta, live in an orphanage. Despite their poverty, Werner is clever and resourceful, and he becomes a favorite of Frau Elena, who runs the orphanage. When he is eight, Werner finds a broken radio and meticulously repairs it. Over time, he becomes adept at understanding how the radio works. With the radio, Werner and the other orphans can hear broadcasts, including news that indicates that the Nazi party is gradually gaining power.
When she is six years old, Marie-Laure loses her eyesight permanently due to a congenital condition. Her father, who works as a locksmith, is determined to help his young daughter thrive. He begins to teach her Braille and shows her how to navigate based on calculations she has memorized. To help her, he begins to build a scale model of their neighborhood. At first, Marie-Laure is afraid and unsure of her ability to ever be able to navigate without sight. However, she eventually becomes skilled at being able to find her way through the streets of Paris.
The novel alternates between events happening in August 1944 and the events that happened in the ten years leading up to that date. This structure creates a sense of mystery and suspense, especially since the events of August 1944 are very dramatic. The impending bombing of Saint-Malo is a tense and plot-driving event, but the unfolding of this action is paused by the flashbacks to events ten years earlier. Some details, such as the presence of the stone that Marie finds hidden in the model house, only make sense in the context of information revealed later in the sections set further in the past. This structure means that readers must patiently and tentatively navigate the plot, waiting for more information to be revealed. This process of readers uncovering information mirrors how Marie-Laure navigates the world. Rather than taking information in all at once using her visual senses, she has to carefully feel her way through, gradually getting clues by using the full range of her remaining senses.