As Nazi storm troopers march into Krakow, Poland, in the fall of 1943, 11-year-old Romek (Oscar nominee Haley Joel Osment) is spirited away from his doomed Jewish family by a peasant farmer who agrees to hide him. Hidden in a potato sack, Romek's adventure begins.

The farmer, Gniecio, smuggles Romek to his small village in Easter Poland. Though presented as a distant cousin, it is not long before the family discover Romek's Jewish heritage. Bright and sensitive, Romek is detested by the family's 12-year old son, Vladek, and befriended by the family's saintly younger brother, Tolo.

The local priest (Oscar nominee Willem Dafoe) coaches Romek in the Catholic religion while respecting the Jewish heritage which Romek must ignore if his life is to be saved. Soon the impressionable child is witness to the abject cruelty of the invading Nazis-witnessing not only the priest's humiliation but also the execution of their neighbors.

Tormented by Vladek and some of the neighborhood boys, Romek seeks solace in games. Together with Tolo and Maria (a young girl who introduces Romek to romance) they act out the mystic roles of Christ and his disciples, whose lives they have studied with the Priest.

While vainly attempting to hide in his imaginary world, the children are forced to witness the reality of trains carrying thousands to the death camps. They see escaping prisoners robbed by local farmers. Finally, they begin to fight back after Tolo and Vladek's father, Gniecio, is killed for illegally hiding a pig.

Despite the cruelty of the apocalyptic world around them, the children finally learn to accept and treasure each other in the hope of surviving another day.