Set in occupied France during World War II, the novel centers on a blind French girl and a German boy whose paths cross.
In 1934, Marie-Laure LeBlanc is the daughter of a widowed master locksmith at the Museum of Natural History in Paris whom she often accompanies to work. Marie has been suffering from rapidly deteriorating eyesight until eventually becoming fully blind by cataracts at the age of 6. Her father promises that he will always be there for her and creates a wooden scale-model of their neighborhood in Paris for her to memorize by touch so that she is able to navigate by herself. He also keeps her mind sharp by hiding birthday gifts in intricate puzzle boxes that he carves. Marie also learns to read Braille and aside from her birthday gifts, she receives new novels in Braille for her to read. She becomes entranced by the imagined world like those that she explores in her Braille edition of Jules Verne’s Twenty Thousand Leagues Under the Sea.
The museum her father works at is rumored to house a large diamond with "red flames" at its center, the "Sea of Flame". According to legends and rumors, the diamond is cursed and whosoever keeps it, becomes cursed with unending misfortunes along with everlasting life.
Meanwhile, in Germany, 8-year-old Werner Pfennig is an orphan in the coal-mining town of Zollverein. He and his sister Jutta find a broken short-wave radio behind the Children’s Home where they live. Werner manages to repair the radio and his natural skill for circuitry becomes apparent.
When the Nazis invade France in 1940, Marie-Laure and her father flee to the coastal town of Saint-Malo to take refuge with her great-uncle Etienne, a recluse still suffering shell-shock from the Great War. Unbeknownst to Marie-Laure, her father has been entrusted with the Sea of Flames or one of three exact copies, all of which must be hidden to keep them out of the Germans’ hands. He conceals it in a model he makes of Etienne’s house and street in Saint-Malo. But shortly thereafter, he is arrested by the Germans and disappears, leaving Marie-Laure alone with her great-uncle Etienne and his housekeeper. Soon, a Nazi treasure-hunter by the name of Sergeant Major Reinhold von Rumpel sets out on the trail of the Sea of Flames.
Werner's passion for science and his gift for radio mechanics earn him a place at a nightmarish training school for the Nazi military elite where, he’s told, “You will all surge in the same direction at the same pace toward the same cause. . . . You will eat country and breathe nation.” Werner obeys, and when he graduates, his discipline and scientific aptitude carry him into the Wehrmacht, where he proves adept at finding the senders of illegal radio transmissions. But he’s increasingly sickened by what happens when he tracks a radio signal to its source: “Inside the closet is not a radio but a child sitting on her bottom with a bullet through her head.” And he’s haunted by his memories of the Frenchman’s broadcasts, which remind him of a time when science seemed an instrument of wonder, not of death.
His path and Marie-Laure’s converge in 1944, when Allied forces have landed on the beaches of Normandy and Werner’s unit is dispatched to Saint-Malo to trace and destroy the sender of mysterious intelligence broadcasts. Werner ultimately decides to allow the broadcasts to continue unmolested and eventually saves Marie-Laure from von Rumpel. Although only together for a short amount of time, they form a strong bond. Werner sends Marie-Laure into safety but becomes gravely sick. Although he seems to recover, Werner mistakenly enters a field of landmines at night and ends up triggering a mine that ends his life.
30 years later, Jutta receives information from an old associate of Werner's that contains information on his death as well as a piece of the model that Marie-Laure's father had made. This piece of model may or may not contain the Sea of Flames at this point in the story. Jutta travels to France with her son Max where she meets up with Marie-Laure at the museum at which her father had worked. Marie-Laure discovers that the Sea of Flames was left in a hidden grotto in Saint-Malo by Werner before he died. The story ends with Marie-Laure, now 86 years old, walking with her grandson in the streets of Paris where she grew up.