In the modern day city of Salem, known as Naumkeak to the Native Americans, a group of English settlers arrive. It is the early 1600's, and Mary performs a love ritual in the forest. She is expecting someone to come find her, and, with the help of that ritual, that person will be her "true love". Expecting a man named Charles Brown, the fellow Native American Hobomok arrives on the scene instead.
The white settlers make themselves at home in Salem, working for the London Company, which has just received an order to fulfill. When the news breaks that a massive fight has erupted between Native Americans and the white settlers, Hobomok tries to calm things down. Despite his best efforts, nothing works.
Throughout the novel, Hobomok continues to fall deeper in love with Mary, who he invites on a ritual Native American hunt. Though Mary needs to have permission to go from her father, she is allowed to come along. She is shocked when Hobomok reveals his true self in the wild - unafraid and willing to do anything to catch an animal.
Mary receives a letter that Charles Brown is dead, which makes her break into tears. She slowly grows crazy because she knows she can no longer marry him, and doesn't truly want to marry Hobomok. Three years later, it is revealed that Charles Brown did not actually die, and was simply taken prisoner. He escapes imprisonment, and he and Mary instantly get married, to the disapproval of Hobomok.