William Fletcher is in love with his cousin Alice, much to the chagrin of Fletcher's father, who believes Alice is a bad match because she holds differing religious views than they do. When Fletcher and Alice run away to spend their lives together, they are caught and returned, and Alice is forced to marry Charles Leslie. Fletcher is devastated, and he decides to rebuild his life by moving from England to the English colony at Massachusetts Bay. He marries an orphan there, but he still loves Alice who now has two kids with Charles: Faith and Hope. One day he receives word that Alice and Charles have died, and he is next of kin, so the children will move to Massachusetts Bay to live with him.
To help around the house, the village provides two Native American slaves for Fletcher, Magawisca and Oneco. Everell, Fletcher's firstborn son sees Magawisca sneaking out, but he gives her the benefit of the doubt, choosing to believe the best about her. When Fletcher goes to the coast to conduct business with merchants, he keeps Hope with him and sends Faith back home. Magawisca's suspicious behavior is connected to an impending Native raid, and she worries about Faith's well-being, but she can't say anything without subverting her tribe's plans to kill the settlers. Inevitably, the tribe attacks, killing Fletcher's wife, kidnapping Faith to be raised by the tribe. When Mr. Fletcher returns, he mourns for a while before returning to normal.
When the Natives decide to sacrifice Everell to the gods, Magawisca tries to help, but to no avail. Mononotto, the tribe's chief has decided to take Everell's life as recompense for his own son who was savagely murdered by the settlers. Magawisca drugs her guard with strong sleeping tea before escaping to find the tribe, readying the sacrifice. As her father Mononotto swings, she intervenes, and he cuts off her arm by mistake, allowing Everell to go free. Nelema is tried for witchcraft for her herbal medicine, but Hope helps her escape, leaving to live in Boston for a while with the settlers there. Everell leaves the community, but eventually moves back, this time to live with the Fletchers in Boston.
Hope is friends with Esther Downing who tells of Everell's powerful integrity and character, and Hope starts to realize that there is an attraction between the two of them. William Fletcher and Hope were hoping that Everett would marry Hope, his half-sister. The famous Bostonite family, the Winthrops, also have intentions for her to marry, but their pick is Sir Philip Gardiner, but the knight has a page who is secretly his lover, crossdressing as an apprentice.
One night after a date with Sir Philip to a legal lecture, Hope meets Magawisca in a graveyard where she learns that Faith has married and converted to Catholicism, and Hope hopes to visit soon, but Magawisca warns Hope that her sister has become a different kind of person than she used to be.
Hope wrongly concludes that Everell likes Esther, and she accidentally overlooks his affection for her. She does admit to Philip that she won't marry him, but he comes with her anyway when she goes back to meet Magawisca, ambushing her meeting with the natives. In the commotion, Sir Philip takes Magawisca captive, and Oneco takes Hope. When Oneco and Mononotto his father head off toward their camp, Mononotto is struck by lightning, allowing Hope to escape. She is chased by ravenous sailors, but when she finds refuge in a boat, she is discovered by Antonio who thinks she is the Virgin Mary or a saint. She allows the misconception, and he rows her to shore.
She visits Magawisca in jail to help her escape, so long as she takes Rosalin. Sir Philip dies in the hands of a man named Morton. Everell attempts to save Magawisca, but Hope actually succeeds, leaving an imposter in her place. When Hope is discovered to be missing in the aftermath, the reader learns that Esther, convinced that Hope belongs with Everell, has left the two to elope, and they do exactly that.
