All the Light We Cannot See is structured nonlinearly; sections taking place during the Battle of Saint-Malo in August 1944 are interspersed with sections about earlier times starting in 1934 and going in chronological order. Additionally, the point of view alternates between Marie-Laure LeBlanc and Werner Pfennig between chapters. For simplicity, their respective narratives preceding the Battle of Saint-Malo along with the events during and after the battle have dedicated sub-sections.
Marie-Laure LeBlanc is a girl who lives in Paris with her father Daniel, the master locksmith at the Museum of Natural History. She went blind at the age of six in 1934. Since then, Daniel has helped her adapt to her blindness by creating a model of Paris for her to feel and training her to navigate it. Marie-Laure hears stories about a diamond known as the Sea of Flames that is hidden within the museum; the diamond is said to grant immortality at the cost of endless misfortune to those around the owner. The only way to end the curse is to return the stone to the ocean, its rightful owner.
When Nazi Germany invades France in 1940, Marie-Laure and Daniel flee to the coastal town of Saint-Malo to take refuge with her great-uncle Etienne, a reclusive, shell-shocked veteran of World War I who spends his time broadcasting educational audio recordings, produced by his deceased brother, across Europe. Unknown to Marie-Laure, the museum has entrusted her father with either the Sea of Flames or one of three exact copies that were made to protect the original gem. Months later, while building a model of Saint-Malo for Marie-Laure, Daniel is arrested and suspected of conspiracy. Other than a few letters he manages to get out of prison, he is not heard from again, leaving Marie-Laure alone with Etienne and his longtime maid and housekeeper, Madame Manec.
Madame Manec participates in the French Resistance along with other local women. Their activities have some success, but Madame Manec becomes ill and dies. Marie-Laure and Etienne continue Madame Manec's efforts over the next few years, transmitting top-secret messages by radio transmitter. Eventually, while Marie-Laure is going home to deliver a routine Resistance message from the bakery, she is visited by Sergeant Major Reinhold von Rumpel, a Nazi gemologist who is searching for the Sea of Flames and has tracked the real one to Saint-Malo. Von Rumpel, who is dying of cancer, believes the diamond (according to the myth) will save him. Von Rumpel asks the frightened Marie-Laure if her father left her anything and leaves when she says "just a dumb model". Etienne takes over Marie-Laure's role of message-deliverer, and she later opens the model of Etienne's house on the Saint-Malo model and finds the Sea of Flames. Etienne is eventually arrested and sent to Fort National on false charges of terrorism.
In Nazi Germany, Werner Pfennig is an orphan in the coal-mining town of Zollverein. He is exceptionally bright and has a natural skill for building and repairing radios. He discovers this skill in 1934 at the age of eight after he finds a broken radio with his sister Jutta, fixes it, and uses it to hear science and music programs transmitted across Europe. In 1940, Werner's skill earns him a place at the National Political Institute of Education at Schulpforta, a draconian state boarding school teaching Nazi values, which Jutta hates. She has been listening to French radio broadcasts about Germany's war crimes during its invasion and is angered by Werner's accepting a place at Schulpforta. Before leaving for Schulpforta, Werner promises Jutta he will return to Zollverein in two years to fly away with her on an airplane.
In Schulpforta, Werner begins working on radio technology alongside Frank Volkheimer—a strong student perceived by the other students as the ideal Nazi—under the supervision of Schulpforta professor Dr. Hauptmann. Volkheimer eventually leaves to join the military. Werner befriends Frederick, a kind-hearted and inattentive student who is deemed weak by the school. After enduring bullying, Frederick suffers a severe beating at the hands of his fellow students, leaving him with permanent brain damage and forcing his return to his home in Berlin. Two years after entering, when Werner asks to leave Schulpforta, Dr. Hauptmann lies about Werner's age and persuades Nazi officials to send him to the military.
Werner is placed in a Wehrmacht squad led by Volkheimer that consists of engineer Walter Bernd and two other soldiers, both named Neumann. The squad travels throughout Europe, tracking illegal enemy signals and executing whoever is producing them. During this time, Werner also contracts an illness, a fever, from which he never fully recovers. Werner becomes increasingly disillusioned with his position, especially after his group kills an innocent young girl after he incorrectly traces a signal. When the squad reaches Saint-Malo, Werner traces Etienne's signal. Recognizing the voice and music to be from the science programs he listened to at the orphanage, he does not disclose the signal. Werner tracks it to Etienne's house and becomes entranced by Marie-Laure when he sees her heading to the bakery. Werner decides to conceal the signal's existence from the rest of the squad.
When the United States forces lay siege to Saint-Malo in August 1944, Marie-Laure grabs the Sea of Flames and hides in the cellar. After waking the next day, Marie-Laure leaves the cellar to get some water. When von Rumpel enters the house, looking for the Sea of Flames, Marie-Laure hides in the attic for several days. Using Etienne's transmitter, she tries to call for help by transmitting herself reading a braille version of the science fiction novel Twenty Thousand Leagues Under the Seas alongside pleas for rescue. During this, an ill and increasingly desperate von Rumpel unsuccessfully searches the house for several days after discovering the Sea of Flames is no longer inside the Saint-Malo model.
Meanwhile, Werner, Volkheimer, and Bernd become trapped beneath a pile of rubble in a cellar after the U.S. forces bomb the hotel in which they have been staying. Bernd is wounded in the explosion and dies. Werner mends a radio in an attempt to find help and discovers Marie-Laure's broadcasts. Several days later, Volkheimer realizes they could die soon and has Werner blow up the rubble with a grenade. After they escape, Werner goes to Etienne's house to rescue Marie-Laure. He finds von Rumpel, who has become delirious after failing to find the Sea of Flames. After a brief standoff, Werner shoots and kills von Rumpel and meets Marie-Laure. As they flee from Saint-Malo, Marie-Laure places the Sea of Flames inside a gated grotto flooded with seawater to return the gem to the sea. She gives the key to the gate to Werner, who sends her away to safety. Werner is captured and sent to a US prisoner-of-war camp, where he, after never fully recovering from his initial fever, becomes gravely ill. One night, in a fit of delirium, Werner leaves the hospital tent and accidentally steps on a German landmine, which kills him instantly. Etienne is freed from Fort National and reunites with Marie-Laure. They never discover what became of Daniel, her father.
Thirty years later, Volkheimer receives Werner's belongings at the time of his death, including the model house that contained the Sea of Flames. Volkheimer finds Jutta, who is now a married math teacher, and gives her the items. He tells her that Werner was last seen in France and may have been in love. Jutta travels to France with her son Max to investigate the model and meets Marie-Laure in Paris; she is now working as a marine biologist at the Museum of Natural History. Marie-Laure opens the model and finds the key to the grotto. She wonders where the gem ended up; whether it stayed in the ocean or whether Werner took it with him. The story ends in 2014 with Marie-Laure, now eighty-six years old, walking with her grandson Michel in the streets of Paris.
