Charlotte Gray is the story of a young Scottish woman who travels to London in early 1942 to help in the war effort, almost two years after the German invasion and occupation of northern France. She takes a job as assistant to a doctor, but the role makes little use of her talents.
At a party, she meets an RAF fighter pilot called Peter Gregory, and they fall in love. He is sent on a secret mission into southern France (the "Free" or Vichy zone) while bilingual, Francophile Charlotte is recruited and trained by British intelligence to work as a courier in France. Peter is declared missing just as Charlotte is sent on her first mission. Once she has completed her deliveries of radio crystals and an agent, she elects to remain in France against orders and search for Peter.
Charlotte settles into a new French life in the southern village of Lavaurette, using her undercover identity as Dominique Guilbert. She loves the spirit of rural France, and feels more at home here than she did in her small shared flat in blitz-ravaged London. While she sets about trying to track down Peter, she befriends a local resistance member, Julien, and takes a job as housekeeper to his father, an eccentric but engaging Jewish artist named Levade to whom she grows very attached. Charlotte also takes an interest in two young Jewish boys whose parents have been deported, presumably to the death camps in Poland. The Duguay boys are being concealed from the collaborating Vichy regime by Julien and his friends.
The relatively easy life in the "free" Vichy zone comes to an end when the Germans, worried by Allied victories in North Africa, occupy the south of France as well. Under their direct command, the Vichy French are now forced to fulfil German quotas for Jewish deportation, and Levade - a decorated veteran of World War I - is rounded up. He is transported to a holding camp at Drancy near Paris under the impression that it was his own son who betrayed him. Charlotte travels to Paris and tries to see him to explain the truth - that Julien had to betray his father (and himself) to protect the Duguay boys - but Levade dies of pneumonia without receiving the message. Julien's self-sacrifice is anyway in vain, for the Duguay boys are discovered and sent via Drancy to Poland, where they die in the gas chambers.
Charlotte fails to locate Peter during her several months in France. She contributes to one resistance effort, but otherwise spends her time keeping house, not quite falling for Julien, and trying to keep her blonde hair dyed a suitably French colour. After her final failure at Drancy, she returns to England with the help of an intelligence asset in Paris.
Peter Gregory makes it back to England, despite an injured leg, travelling via North Africa with the help of an American and an Italian sympathiser.
Charlotte visits her parents in Scotland, resolves a traumatic childhood misunderstanding with her father, and then returns to London where she is reunited with Peter. Both of them have changed, but their love has survived their time in occupied France.