Set in Nazi-occupied Kraków, Poland, during World War II, the story follows nineteen-year-old Emma Bau, a young Jewish woman forced to assume a false identity and work for a high-ranking Nazi official while secretly aiding the Jewish resistance.
Emma narrates from the present moment of her double life: walking through the city center with Lukasz, a three-year-old Jewish boy she is hiding, both posing as gentile Poles. In flashbacks, she recalls meeting her husband, Jacob Bau, a physics student and son of a prominent sociologist, while she worked at the university library. Despite the gap between his wealthy, secular family and her poor, Orthodox background, they married hastily in late summer 1939 as war loomed.
Weeks after the wedding, Germany invades Poland. Emma loses her job and Jacob is barred from the university. He joins the underground resistance and soon tells Emma he must disappear. He instructs her to remove her wedding rings, destroy their marriage certificate, and deny their marriage. Emma hides the certificate instead and wakes the next morning to find him gone after only six weeks of marriage.
Emma returns to the Jewish quarter, Kazimierz, but discovers her parents have been forced into a walled ghetto in Podgorze, a district across the river. She voluntarily enters the ghetto and finds her parents, Chaim and Reisa, in a squalid one-room apartment. Assigned to work in an orphanage, she befriends Marta Nederman, the spirited daughter of a coworker. Marta brings Emma to a weekly Sabbath dinner where she meets Alek Landesberg, the leader of a Jewish resistance group, and his associate Marek. Alek reveals he knows Jacob and promises to relay word that Emma is safe.
Emma witnesses a Nazi soldier shoot a pregnant woman in the alley below her window. The woman's young blond son stands motionless over his mother's body. The killing destroys Emma's ability to deny the violence around her. Alek later delivers a coded note from Jacob confirming he is alive and on a weapons-procurement mission.
One night, a stranger smuggles Emma out through a crack in the ghetto wall, leaving her parents behind. He leads her to the home of Krysia Smok, Jacob's Catholic aunt by marriage, a former socialite living on the outskirts of the city. Krysia gives Emma forged papers under the name Anna Lipowska, a gentile orphan, along with a gold cross necklace. The next night, Lukasz arrives: the blond son of the murdered woman, the last descendant of a great rabbinic dynasty. He is to pose as Anna's younger brother.
Krysia hosts a dinner party to establish Emma's cover. Among the guests is Kommandant Georg Richwalder, the second in command of the Nazi General Government in southern Poland. Emma feels a powerful, unsettling attraction to this towering man with battle scars from the First World War. Fascinated by her intelligence and fluent German, the Kommandant offers Emma a job as his personal assistant at Wawel Castle, the Nazi headquarters. Krysia urges her to accept, believing proximity to the Kommandant could benefit the resistance.
At Wawel, Emma manages the Kommandant's correspondence while enduring the jealousy of Malgorzata Turnau, the reception secretary. Alek tasks Emma with stealing blank security passes from a colonel's office safe. She succeeds over several visits, delivering the passes along with silver coins from Krysia to fund the resistance.
Alek tells Emma her mother is gravely ill in the ghetto. A delegation of senior SS officials, members of the Nazi paramilitary and security organization, visits Wawel, and Emma notices a map with a large X drawn through the ghetto. That evening, the Kommandant returns from Auschwitz, a Nazi concentration camp in southern Poland, visibly shaken. As Emma grows closer to the Kommandant, Alek raises the stakes: He needs her to infiltrate the Kommandant's home study for classified documents. Getting access, he implies, will require Emma to become intimate with the Kommandant.
Emma agonizes over the betrayal of her marriage but resolves to act. She and the Kommandant sleep together, and their affair becomes a pattern: dinners and nights at his apartment, where she searches his papers while he sleeps but finds nothing significant.
Krysia warns that a resistance informant has been leaking information. When the Kommandant travels to Warsaw, Emma breaks into his apartment and discovers classified documents revealing the Nazis plan to liquidate the Kraków ghetto and send Jews directly to death camps at Auschwitz and Belzec by January. She takes carbon copies. The Kommandant's driver, Stanislaw, who quietly sympathizes with the resistance, catches her leaving with papers visible but lets her go.
Emma delivers the documents to Marek at a riverside cabin. On a snowy night soon after, Jacob knocks Emma down on the street, saving her from walking into a patrol by the Gestapo, the Nazi secret police. He leaves an amber stone in her pocket as a sign. Weeks later, Jacob appears at Krysia's kitchen. They reunite and make love, but Emma is tormented by guilt over the affair. Jacob implies the resistance is planning something dangerous. Minutes after he leaves, two Gestapo officers arrive asking about him by name. Krysia stalls them and secretly radios for help; the officers are recalled on a fabricated emergency.
At a final meeting, Alek reveals that Auschwitz is a death camp where thousands are gassed daily. He also discloses that the Kommandant's wife, Margot, was half-Jewish; her father was a Jewish political activist executed at Bergen-Belsen, a Nazi camp in northern Germany, after the Kommandant refused to intervene. Margot shot herself with his revolver while six months pregnant.
The resistance bombs Warszawa Café, a popular Nazi bar, killing seven officers. Marta tells Emma that Jacob was seriously injured in the blast but is alive. Emma reads a classified telegram at work confirming Alek was shot and killed while resisting arrest.
Months later, Krysia realizes Emma is pregnant. Emma does not know if the child is Jacob's or the Kommandant's. Krysia declares the child will be Jewish and Jacob's, regardless. When Malgorzata accidentally sees Emma's belly, she tells the Kommandant, who is overjoyed and plans to send Emma to his sister in Austria the next morning. Krysia arranges an alternative escape through the resistance.
That final night, Emma drugs the Kommandant's brandy and slips out to the ghetto wall. Through a hole, she finds her emaciated father, who tells her that her mother died ten days earlier. He returns her wedding rings and marriage certificate. She tells him she is pregnant; he whispers "Mazel tov," and they say the mourner's prayer together before he disappears into the darkness.
On the railway bridge, the Kommandant, who has woken early from the sedative, catches Emma. Her rings and marriage certificate tumble from her pocket, and he realizes she is Jewish. Devastated, he raises his gun. Emma accuses him of killing Margot through his inaction. Before he can fire, Marta shoots him from the shadows. He fires back, wounding Marta gravely. Emma holds the Kommandant as he dies, telling him she loves him and meaning it.
Marta, unable to walk, tells Emma that Jacob is hidden at a farm in Czernichow, a village beyond the forest, and insists Emma leave her behind. Stanislaw drives Emma to Krysia's house, where she finds the Gestapo has ransacked the home and Krysia lies dead. Emma finds Lukasz hiding in the attic and carries him out.
At dawn, Emma and Lukasz walk into the forest. She puts her wedding rings back on, reclaiming her identity. From the forest edge, she spots the farm where Jacob is hidden. She and Lukasz descend toward reunion with her husband, Emma carrying an unborn child she has already decided to name Alek.