As children in the loving Ekdahl family, Fanny and Alexander enjoy a happy life with their parents, who run a theater company. After their father dies unexpectedly, however, the siblings end up in a joyless home when their mother, Emilie, marries a stern bishop. The bleak situation gradually grows worse as the bishop becomes more controlling, but dedicated relatives make a valiant attempt to aid Emilie, Fanny and Alexander.

British stockbroker Nicholas Winton visits Czechoslovakia in the 1930s and forms plans to assist in the rescue of Jewish children before the onset of World War II, in an operation that came to be known as the Kindertransport.

Successful surgeon Tomas leaves Prague for an operation, meets a young photographer named Tereza, and brings her back with him. Tereza is surprised to learn that Tomas is already having an affair with the bohemian Sabina, but when the Soviet invasion occurs, all three flee to Switzerland. Sabina begins an affair, Tom continues womanizing, and Tereza, disgusted, returns to Czechoslovakia. Realizing his mistake, Tomas decides to chase after her.

The story of Michael Berg, a German lawyer who, as a teenager in the late 1950s, had an affair with an older woman, Hanna, who then disappeared only to resurface years later as one of the defendants in a war crimes trial stemming from her actions as a concentration camp guard late in the war. He alone realizes that Hanna is illiterate and may be concealing that fact at the expense of her freedom.