Sixteen-year-old Katherine (Kit) Tyler lived with her grandfather until his death in 1687. Without a chaperone, 16-year-old Kit, an orphan, leaves Barbados, an island country in the West Indies, and sets sail for a Puritan colony in Connecticut. Kit’s grandfather was a royalist who considered Puritans to be English traitors, so she had never met her aunt’s family. Although not invited to her aunt’s home, she hopes to live with her relatives — Rachel and Matthew Wood.
During Kit’s five-week journey aboard the Dolphin, Kit meets Nat, the captain’s son. She also meets Goodwife Cruff, who accuses Kit of being a witch after witnessing Kit’s swim in the harbor to retrieve a toy that belonged to Prudence, the woman’s daughter. Nat later tells Kit that according to the Puritans, only witches can stay afloat; the innocent ones sink — an omen of events to come.
The solemn New England settlement turns out to be plain and rough, filled with hardworking people, which is a severe contrast to Kit’s privileged lifestyle that included extravagant clothes and servants. Everything must be made from scratch, including soap and wool, and leisure is not a part of the Puritan culture. Kit desires to help her cousins, Judith and Mercy, with the chores, yet because of her upbringing, she struggles against doing the work of slaves.
To escape the never-ending work, Kit agrees to teach basic literacy classes to the children at the dame school. But when she has the children act out a Bible story, the schoolmaster angrily dismisses her. In despair, she flees to Blackbird Pond — a setting that gives her a sense of peace. Here she meets Hannah Tupper, an old widow reputed to be a witch. Years ago, the Puritans branded Hannah’s and her husband’s foreheads because they were Quakers. Hannah, an outcast from the Puritan settlement, quickly comprehends Kit’s feelings of grief, loneliness and frustration, and a friendship forms between them in spite of her aunt and uncle forbidding the relationship. Nat Eaton is also a friend of Hannah’s, and he and Kit cross paths from time to time at the widow’s house. Kit’s other chance at escaping the drudgery of her new life lies in the possibility of marriage to a wealthy young man, William Ashby, who has taken an interest in her.
Eventually, John, who visits the family so frequently that he is considered a part of the family, enlists in the militia and leaves. Shortly after, a plague strikes the settlement. Kit, Mercy, Judith and her aunt come down with the fever. Kit recovers first, and she tends everyone and everything in the household.
A mob comes to the Wood home wanting Matthew to go with them to get Hannah, who they think is a witch and the one responsible for the fever that has killed three people. Kit secretly leaves to warn Hannah. She, and later Nat, help Hannah escape aboard the Dolphin.
When Kit becomes the target of the mob’s blame, she is arrested for witchcraft. Facing the possibility of having her ear cut off, branding or hanging, Kit endures a trial of charges for befriending a witch and other trumped up charges. Just when conviction appears certain, Prudence Cruff enters the courtroom, escorted by Nat, and testifies that Kit taught her to read and write. After Prudence astonishes the court by reading a Bible passage, Kit is declared innocent.
Subsequently, William resurfaces in Kit’s life, but his concern for appearances outweighs his feelings for Kit, and the relationship ends. John returns from war and makes known his affection for Mercy. William’s interest in Judith returns, and they marry. Kit makes plans for her life with Nat, now captain on his newly built ship, the Witch.