All the Light We Cannot See follows the lives of Marie-Laure LeBlanc and Werner Pfennig during a period of time surrounding World War II. The novel alternates between time periods, starting in medias res, during the bombing of Saint-Malo, France in August 1944, and then going back to tell the history of the two protagonists starting in 1934.
Marie-Laure is a young girl who lives with her father in Paris. Her father is a locksmith for the Museum of Natural History. Marie-Laure goes blind at the age of 6 because of cataracts in her eyes. Her father patiently helps her deal with her blindness by giving her Jules Verne novels in braille and by creating a wooden replica of their neighborhood so that she can learn to navigate their neighborhood in Paris despite her blindness.
The second main character, Werner Pfennig, grows up in Zollverein, Germany with his sister, Jutta. They live in an orphanage that is run by a French nun, Frau Elena. Werner is very intelligent, curious, and gifted when it comes to science and engineering. He finds a broken radio and manages to fix it; he and his sister use it to listen to radio broadcasts about science. Werner dreams of becoming a scientist, but due to his social class as a poor orphan, he will be required to work in a coal mine as soon as he turns 15. He gets a chance to escape this fate when he fixes a radio for a Nazi official and is offered a position at a Nazi school in Saxony, Schulpforta.
The rumors of the approaching German occupation grow and the museum prepares for an invasion, making 3 replicas of a priceless diamond named the Sea of Flames. The Sea of Flames is rumored to have a curse surrounding it: the one who keeps it will live forever, but all those he loves will suffer. After the bombing of Paris, Marie-Laure and her father flee the city, her father carrying the Sea of Flames, or a replica—Daniel LeBlanc does not know whether he carries the real or a fake. When her father discovers that the man to whom they were supposed to deliver the diamond has fled the country to go to London, they decide to continue to the house of her great-uncle Etienne in Saint-Malo. Her father once again builds her a model of the city and hides the diamond inside the replica of their house, unbeknownst to anyone, including Marie-Laure. The Germans confiscate all of the radios in Saint-Malo, but Etienne manages to keep one hidden in his attic. Marie-Laure's father is asked to return to the museum but is arrested en route and is placed in a prison camp in Germany.
A Sergeant Major named Reinhardt von Rumpel is given the task of finding and cataloging cultural artifacts wanted by Hitler; the Sea of Flames is the object von Rumpel most wants to find. He at first just wants it for its value to the Reich, but later wants it for personal reasons: to save him from his fate of dying of cancer.
Werner struggles in the environment at Schulpforta, where is only friend is a kind gentle boy named Frederick. Frederick is eventually singled out for punishment because he refused to participate in killing a prisoner. He is badly beaten and nearly dies. He is sent home because his brain has received permanent damage. Werner's skills in math and science are noticed by a teacher, Dr. Hauptmann, who then trains Werner to design a system that can help him locate radio broadcasts. Werner is watched over by an older student, Volkheimer, who is known for his large, intimidating stature and rumored toughness.
Madame Manec, Etienne's housekeeper, organizes a group of women who fought for the resistance against the Nazis. She attempts to get Etienne onboard, but he feels that it is too dangerous. However, after Madame Manec's death, Etienne and Marie-Laure feel compelled to continue her efforts of resistance. Their method involves Marie-Laure going to a bakery in town where she gets loaves of bread from Madame Ruelle that have slips of paper with resistance intelligence baked on the inside. The information is then delivered to Etienne, who broadcasts them on his radio. Near the climax of the novel, Etienne is arrested when he attempts to discover the locations of Nazi anti-aircraft guns to broadcast.
As the war continues, Werner is told he is 18 instead of 16, a lie perpetrated by Dr. Hauptmann so that that Werner can be sent into the military. He joins a special team, with Volkheimer, that hunts down anti-German radio broadcasts and kills the broadcasters. As the novel approaches the climax of the bombing of Saint-Malo, the team moves to Saint-Malo to try and locate another illegal broadcast. Werner realizes that the broadcast in Saint-Malo seems very similar to the science broadcasts he listened to in his youth. Werner doesn't tell his team about the broadcast. He locates it himself, finding Marie-Laure and falling in love with her.
The Allies bomb Saint-Malo. Werner takes shelter in a hotel cellar with Volkheimer and an engineer; the hotel collapses under the bombing, which traps Werner and the two others. Marie-Laure hides in Etienne's cellar until the bombing is over. She goes to the third floor to find water, but ends up hiding in the attic while a Sergeant Major von Rumpel enters her home in a desperate search for the Sea of Flames.
After spending days in the attic, Marie-Laure begins broadcasting on her uncle's radio. Werner, trapped, manages to fix his own radio, and he and Volkheimer hear her reading. While reading she pauses and says that 'He is here'. Werner understands that she is in danger. Instead of waiting to be discovered, Marie-Laure starts to play loud music. Volkheimer hears the music through his radio and decides to start blasting through the rubble where he and Werner are trapped. Werner manages to get out, and rescues Marie-Laure by killing von Rumpel. He helps her escape the city, but before leaving Marie-Laure put the Sea of Flames and the model of the house in an ocean grotto and gives Werner the key. Marie-Laure reunites with Etienne, and the Allies take Werner prisoner. He becomes ill, deliriously wanders into a minefield, and is killed by an explosion.
In 1945, Werner's sister Jutta is in Berlin, working in a factory with Frau Elena and some other girls, when the Russian soldiers arrive and rape her. Marie-Laure and Etienne move to Paris and search for her father, whom they never find.
Years later, Werner's belongings are given to Volkheimer, who gives them to Jutta. One of the items was the model of Etienne's house. Jutta goes to Saint-Malo to find more information about her brother's final days. She realizes that there is a house that matches the model. Someone puts her in touch with Marie-Laure, who now works at the Museum of Natural History. Jutta and Marie-Laure meet. Jutta tells her that Werner died, and gives her the model house. Inside Marie-Laure finds the key to the gate that protects the grotto. She wonders what Werner did with the Sea of Flames. The narrator reveals that Werner left the diamond in the grotto.
The last chapter tells a short narrative of Marie-Laure in 2014, with her grandson, wondering if souls of the dead travel the same airwaves as the cellphone signals and long ago radio signals, and thus are always with us.