As a young boy in seventeenth-century Portugal, Juan Pereira lived a Christian life with his mother and father, but he often wondered why he was not a choir boy like most of his friends. One fateful night, he discovers the truth: he is of Jewish descent, and his real name is not Juan but Benjamin. That same night, the secret hiding place of the Jews is discovered by the Inquisition, and Benjamin loses his mother and father to martyrdom.

Forced to flee Portugal, Benjamin finds solace in the guidance of Senor Rodriguez, his parents' trusted friend. They search for a safe place for Jews to live, far from the raging fires of persecution. It is in the midst of this search that Benjamin encounters Rachel da Sousa, and they fall in love. Forced to leave Europe to freely live as Jews, the couple takes to the high seas and heads for the New World.

The high seas are dangerous, and the new world isn't much safer. With the help of Samuel, an African slave in search of his lost brother, and Adario, a Huron Native American, Benjamin and Rachel find hope in a free future, but nothing goes as planned. Soon separated, the lovers must find a way to reunite and finally discover a place to call home.