All the Light We Cannot See traces the stories of three characters whose lives intersect during the bombing of the German-occupied French town of Saint-Malo in August 1944. Marie-Laure Leblanc grows up in Paris, where her father, Daniel Leblanc, works as a locksmith at the Museum of Natural History. As a young girl, Marie-Laure goes blind, but her father teaches her to navigate their neighborhood independently by building her a scale model of the neighborhood to learn from. In June 1940, when she is 12 years old, the threat of a German occupation of Paris grows too great to ignore. Marie-Laure and Daniel flee from Paris to Saint-Malo, where they move in with her great-uncle, Etienne, and his housekeeper, Madame Manec.
Unbeknownst to Marie-Laure, Daniel carries a potentially significant item with him when he leaves Paris. The Museum of Natural History owns a legendary diamond called the Sea of Flames. Under the threat of occupation, the museum directors make three copies. Three of the four stones are sent off with various staff members, including Daniel, while the final one remains at the Museum. No one knows if the stone they possess is real or a copy. Once in Saint-Malo, Daniel works to build a scale model of the town so that Marie-Laure can learn to navigate it, and he also hides the diamond in the replica he makes of Etienne’s house. In December 1940, Daniel is summoned back to Paris, and on the journey there, he is arrested. He is taken to a prison camp in Germany, where he eventually dies.
Madame Manec has organized many of the French townspeople into engaging in acts of resistance against their German occupiers. Although Etienne is initially hesitant, he and Marie-Laure eventually begin to take part. Etienne has a special contribution to make: hidden in a secret attic floor of his house is a powerful radio transmitter. Before the war, Etienne used it to broadcast recordings of his deceased brother presenting science programming for children as a way of keeping his memory alive. Now, he uses the radio transmitter to broadcast codes and messages as a way of thwarting the German war effort. This action allows him and Marie-Laure to remain hopeful, even after Madame Manec dies in 1942.
Meanwhile, a boy named Werner Pfennig grows up in an orphanage in Germany with his sister, Jutta. Werner is extremely gifted with mathematical, technological, and scientific knowledge. After he and Jutta find an abandoned radio by accident, Werner teaches himself to repair and rebuild electronics. He is also able to listen to a mysterious French program where a man explains scientific concepts in simple language. As the Nazi party comes to power in Germany, Werner’s talents attract local attention, and when he is fourteen, he is accepted into a specialized training school. He hopes this opportunity will give him a brighter future, but Jutta fears that her brother will be corrupted by Nazi ideology. Indeed, once Werner is at school, he witnesses a lot of cruelty and brutality, including his close friend being beaten until he suffers severe brain damage.
When Werner is sixteen, his age is falsified so that he can serve on the German front lines. He spends the next two years travelling around, tracking down any civilians who use illegal radios in occupied German territory. Werner works alongside a fellow German soldier named Volkheimer. Although Werner tries to ignore the moral conflict he experiences, he is particularly horrified when one of his fellow soldiers kills a woman and young child. By spring 1944, he and his colleagues are sent to Saint-Malo, where he is astonished to discover that a man with the same voice as the one from the program he listened to as a child is broadcasting secret codes. Unsure what to do, Werner keeps this information secret but also spies on the house from which the signal is broadcasted and catches sight of Marie-Laure.
During this same time period, a Nazi official named von Rumpel has been ordered to seize and catalogue jewels from occupied German territories. He becomes obsessed with finding the legendary Sea of Flames, especially because he is suffering from cancer and believes that the diamond will grant him immortality. Between 1940 and 1944, he gradually tracks down three out of four stones, but the genuine one continues to elude him. He finally traces the stone to Daniel Leblanc’s last known residence: Saint-Malo. In August 1944, Allied forces begin bombing Saint-Malo. All three characters are affected by the bombing: Werner becomes trapped in a cellar when a building collapses on him, Marie-Laure is alone in her house, unsure what to do, and von Rumpel seizes the opportunity to go to the house to search for the diamond. When she hears a stranger enter the house, Marie-Laure hides in the attic with Etienne’s radio transmitter, taking the diamond with her. Over the course of four days, she stays hidden, broadcasting messages that Werner receives while trapped in the cellar.
Werner eventually escapes from the cellar and rushes to the house. Von Rumpel believes that Werner is also looking for the diamond, and when he threatens the young soldier, Werner shoots and kills him. Marie-Laure is then finally able to come out of hiding and Werner helps her to get to safety. As they flee the town, Marie-Laure leaves the diamond in a hidden grotto and gives the key to the grotto to Werner. They part ways, and Marie-Laure reunites with Etienne and goes to live with him in Paris. Werner is imprisoned and falls ill. A few months later, while he is delirious, he accidentally steps on a landmine and dies. Years later, in 1974, some of Werner’s possessions are sent to Volkheimer, and Volkheimer takes them to Jutta. Jutta follows these clues to eventually meet Marie-Laure, who has gone on to become a scientist and have a child. Although Marie-Laure wonders if Werner might have gone back to pick up the diamond, it seems most likely that the gemstone was left in the grotto to be washed into the sea.