In the spring of 1944, during the Nazi occupation of France, 13-year-old Lucas Dubois lives as an orphan at a Catholic abbey in the village of Lamorlaye, near the horse-racing center of Chantilly. Found as a newborn in the forest and given a surname meaning "of the woods," Lucas has never known his parents. The other boys call him Petit Éclair, meaning "little pastry," a nickname he earned when he refused to play war games after witnessing a bombing. The name marks him as too soft, and he has internalized the judgment.
One afternoon, Lucas witnesses two older abbey boys, Marcel and Claude, preparing to drown a litter of kittens on a nun's orders. He follows them to a canal bridge and offers his prized fishing lure in exchange for the kittens. Marcel pockets the lure, but Claude throws the sack into the water anyway. Lucas pulls it out, finds five kittens alive and one dead, and hides the survivors in an abandoned stable in the forest above town.
At the stable, Lucas discovers a teenage British girl named Alice, the daughter of a lead trainer at the Great Stables in Chantilly, hiding her thoroughbred horse, Bia. The Germans have ordered all healthy non-racing horses seized for the war effort, and Alice refuses to let Bia be taken. She reluctantly allows Lucas to keep the kittens there, and the two form an uneasy alliance that deepens into friendship. During nightly meetings, Lucas stands watch while Alice exercises Bia, and she gives him riding lessons and English lessons in return.
Lucas also works as a delivery boy for the village greengrocers, which grants him access to Bois Larris, a grand estate the Nazis have converted into a Lebensborn, a secretive maternity program where girls pregnant by German soldiers give birth to babies destined for adoption by German families. Lucas befriends Mme Garnier, the only French staff member, and meets Claire, a young mother whose newborn son, Felix, smiles at Lucas in a moment that loosens something inside him "that he hadn't known was tight" (26). Claire plans to reclaim Felix from Germany after the war and mentions her friend Sabine, who runs a poultry farm on the Oise River where Claire hopes to live with Felix once the occupation ends.
Lucas discovers that Mme Garnier is secretly working for the French Resistance when she accidentally drops a hidden note in front of two German soldiers. Lucas grabs it and bluffs that it contains his delivery instructions. He demands to join her effort, and she agrees: He will carry coded messages disguised as grocery lists between her and Father Gustave, a priest at the abbey. Mme Garnier privately warns Lucas that Claire will never find Felix because the Nazis systematically falsify all adoption records, erasing every trace of the babies' origins. Lucas, who has spent his life wondering whether his own mother was similarly prevented from finding him, is shaken but cannot bring himself to destroy Claire's hope.
Alice reveals her plan to send Bia to Kentucky, where a female horse trainer will prepare the horse for professional racing, something impossible for an unregistered horse in Europe. The plan relies on stolen transport documents: Bia will travel by train to the neutral Spanish port of Bilbao disguised as a registered mare, then board a ship to New York. Alice confides her own dream of going to America, where women can become trainers and people can transcend their origins.
Mme Garnier reveals that she lost her husband and son early in the war and offers to adopt Lucas after the occupation ends. When she moves to hug him, his body flinches, a reflex of a boy who has never been held.
Lucas's resolve hardens when the Gestapo, the Nazi secret police, raids the home of Mme Bernard, a village woman hiding three Jewish children. Lucas watches helplessly as agents drag out the children and the old woman in under two minutes. Soldiers strike a boy with a pistol stock and catch a girl by her hair.
Days later, Lucas arrives at the Lebensborn to find that all the mothers have been sent home and the babies are being removed to Germany immediately. When nurses briefly leave the hallway, Lucas seizes Felix from a row of bassinets, hides him in his grocery tote under carrot greens, and escapes through the kitchen by provoking the cook into chasing him out the back door. An alarm sounds behind him, but the guardhouse guard waves him through.
Lucas hides Felix in an abandoned cottage behind Alice's stable. Alice is furious at the risk to Bia's escape but agrees to help, insisting Lucas maintain his routine so suspicion never falls on him. Mme Garnier, who suspects Lucas, offers him a chance to return Felix anonymously, but he refuses. She silently directs him to infant formula in her supply closet. The Germans cordon off the village and search every train in France.
The arrangement collapses when Hugo, a stableboy from the Great Stables, discovers the stable and bolts to alert the Germans. Lucas delivers one final Resistance message to Father Gustave at the abbey, where Marcel intercepts him with alarming news: The Germans are already searching for a boy matching Lucas's description. Marcel forces Lucas to swap shirts, gives him his cap, and promises to misdirect the soldiers. As they exchange shirts, Lucas sees old scars on Marcel's back and understands the boy's lifelong jealousy: Marcel envied the orphans for having no violent father. Marcel renames Lucas Petit Lion.
Back at the stable, Alice makes a radical decision. She bleaches Bia's mane with hydrogen peroxide to disguise the horse, straps Felix to Lucas's chest, and hands him the groom's passport, ship documents, and directions to the Kentucky farm, sending Lucas in the groom's place to protect both him from capture and Bia from seizure. On the forest training track, Hugo and three German soldiers intercept them, but Lucas dismounts to check Bia's hoof and the soldiers gallop past, prioritizing the search for the baby over a single horse. Bia outruns the lone pursuer. Lucas navigates by compass to the Oise River and at dusk reaches Sabine's poultry farm, the safe haven Claire had described. Sabine sees the shape under his jacket and opens her door.
In Bilbao, Lucas boards the SS Sea Eagle under the groom's name, Gaston Moreau. Moments before departure, Nazi officers arrive demanding to search the ship for both Lucas Dubois and Gaston Moreau. The first mate, who recognizes Lucas, shakes his head at the captain to indicate no one by those names is aboard. The captain declares the officers have no authority on his American vessel and orders the ship to cast off. As the ship pulls away, Lucas wraps his boot in his jacket to simulate a baby and rocks the bundle at the railing so the retreating officers believe he has taken Felix to America. The deception ensures they will abandon the search in France, keeping Felix, Claire, and Sabine safe.
On the open Atlantic, Lucas writes two letters: one to Alice describing Bia's bravery, and one to Mme Garnier confessing everything and claiming her as his mother. He writes that whenever anyone asks about his family, he will say he has "a mother who cares about me and wants the best for me" (265), and signs the letter "Your son." At dawn, he climbs to the highest point on the ship, faces west, and turns in every direction, finding all of them open, clear, and blue.