Bethia Mayfield is the daughter of a Puritan preacher who travels with her family from England to settle in New England. She's a headstrong girl and finds herself breaking a lot of rules in their small, newly established village. She wanders off into the woods one day where she meets a Native called Cheeshahteaumuck. Communicating extensively through signs and facial expressions, they strike up a sort of friendship. She names him "Caleb," namesake of the Caleb in the Bible whom Moses sent into the Promised Land. He gives her the name "Storm Eye" for evident reasons.
Caleb is also a sort of oddball within his culture. Based upon his father's wishes to have him educated, Caleb converts to Christianity in order to be accepted into the Puritan village. In fact, he moves into Bethia's father's house. As a preacher, he is a major town figure and is elected to teach the young men. He sets up a school out of his house where he instructs his own son, Caleb, another Puritan boy, and another Native named Joel. Bethia becomes somewhat jealous of the boys because of their privileged education, since she is tasked to occupy her days with domestic work.
Tragically, the preacher dies on a voyage back home to England and never returns. Alone and unable to provide for themselves, his children are forced to become indentured servants. Bethia is sent to a tutor in Cambridge who is a friend of a friend, but her brother works elsewhere. By good fortune, Caleb and Joel both end up being accepted into Harvard University. They strike up a cheerful friendship with Bethia, which is her only consolation curing this lonely period of her life.
Caleb becomes the first Native American to ever graduate from Harvard. Unfortunately, he and Joel both die shortly after graduation from diseases which the British brought with them to which the Native Americans were not immune. Ultimately, they have both led meaningful lives, however, and make a significant impact on the relationship between Natives and the English in New England. Eventually Bethia falls in love and marries an academic named Samuel. She soon adapts to her life as a wife, surrounding herself with the luxury of books and intellectual discovery.