Having just lost her grandfather, Katherine “Kit” Tyler leaves her home in tropical Barbados on a ship (the Dolphin) bound for Connecticut. There she is determined to find her Aunt Rachel Wood, her only remaining family.
On the ship, she flirts occasionally with the mocking but otherwise good-natured captain’s son, Nat Eaton. She also causes a scene when she jumps overboard to rescue a young girl’s doll. The passengers – especially the girl’s mother, the nosy Goodwife Cruff – are suspicious of any woman who can swim. After the swimming incident, Kit's only companion on the boat is the Puritan John Holbrook, a studious man sailing to Wethersfield to study with the Reverend Gersholm Bulkeley.
Once the ship arrives in Wethersfield, Kit must fess up: her aunt’s family doesn’t actually know she’s coming. Nevertheless, the captain and Nat escort her to the Wood family’s house where she meets her Aunt Rachel, her Uncle Matthew, and her two cousins, Judith and Mercy. Kit’s uncle is a stern man, though once he learns of her orphan status, he begrudgingly allows Kit to stay. What other choice does he have?
Kit is introduced to the laboring life of Puritan New England and all of its tedium. There are chores to attend to and loads of wool to card. Having only worn fancy dresses in the past, Kit must find clothing appropriate to her new station.
Kit also gets to know the Wood family. Uncle Matthew is sometimes harsh, though he is also solid and dependable. He does not agree, we should note, with the King of England’s politics, which is kind of a problem, since it's the 1680s and Connecticut is one of England's colonies. Aunt Rachel was once a beauty, but, as we find out, has lost two sons – a situation that has taken its toll. As for the two daughters, Mercy is kind and patient and suffered from a fever as a child that has left her lame in one leg. Judith is a pretty, prissy flirt, though generally nice.
Time for boy-talk: Judith has her eyes set on William Ashby, the richest, most eligible young bachelor in town. One day at church, however, William sees Kit dressed in all of her finery (that is, fancy dress) and takes a definite liking to her. He asks Uncle Matthew if he can come and call on Kit. Judith doesn't seem to mind much, and instead sets her cap for John Holbrook – whom she meets at church – instead.
One day during work in the fields (which Kit hates, by the way), Kit sees a woman down at Blackbird Pond. It’s Hannah Tupper, Judith explains, a Quaker with a brand on her forehead. The woman could be mistaken for a witch, Kit admits. She feels, though, that the Meadows – the place where Hannah lives – are a space of peace and quiet. She feels at home there, much more so than she has anywhere else in Wethersfield.
William begins to call on Kit, though the two really have nothing at all to talk about. Kit likes the idea of marriage to a wealthy man, though, since it will get her out of the hard labor of the onion patch. John Holbrook starts coming along as well, and everyone assumes he is crushing on Judith. (Little do they know…)
As the seasons turn, Mercy and Kit are tapped to run a schoolroom out of the Wood family house. Kit is thrilled with this opportunity to earn her keep (and to get out of that darn onion patch). Everything is going well until one day Kit decides to have the children playact a skit from the Bible: the parable of the Good Samaritan. Unfortunately, this is the same day that the headmaster is coming to visit. The man is shocked by the liberties Kit takes with the Bible. (Puritans, famous for being stuffy, thought playacting was a huge no-no.) He dismisses the school, fires Kit, and threatens to suspend Mercy as well.
Upset, Kit runs to the Meadows – that place of peace and quiet – where she cries until she falls asleep. When she wakes she meets Hannah Tupper, witch of Blackbird Pond herself, who takes Kit into her house and gives her some delicious blueberry cake. Hannah is extremely kind, it turns out, and owns some very adorable cats. The two women become fast friends. Emboldened (that means that she gained courage) by her new friendship, Kit approaches the schoolmaster and asks him not to suspend Mercy. He agrees, and gives Kit her job back too. Kit and Mercy continue to teach at the school, but Kit is much more careful now.
One day Kit meets Prudence, the girl whose doll she rescued from the ocean, lurking outside. Prudence’s mother won’t let her take lessons at the school (her mother thinks she dumb and can't learn), but Kit convinces the girl to meet her in the Meadows for secret private lessons. Kit lets Prudence borrow her silver horn book (a tiny paddle with the alphabet listed on it), which she keeps at Hannah house. She introduces Prudence to Hannah and the two become friends over blueberry cake and kittens.
New information: Kit learns that Nat, the captain’s son, is also a friend of Hannah’s. He visits her from time to time. He does chores for Hannah, helps her around the house, and brings her presents from his voyages. During one of these visits, Nat and Kit thatch Hannah’s roof together and share a semi-bonding moment. Nat ends up walking Kit home, where he (much to Kit’s embarrassment) meets the Wood family. Uncle Matthew ends up finding out that Kit has been visiting Hannah Tupper. He forbids her from seeing the old woman again.
Kit also learns – through the power of observation – that Mercy is secretly in love with John Holbrook. Well, as luck would have it, John confesses to Kit one day that he is also in love with Mercy – and will be asking for her hand in marriage. Hot dog!
The town’s cornhusking party rolls around and John totally botches his engagement attempt. Judith, who's rather pushy, thinks he is asking for her hand in marriage and the deal ends up being sealed by Uncle Matthew. Kit is the only one who knows the truth: that John wanted to ask for Mercy’s, not Judith’s, hand in marriage. William asks Kit about their own courtship around this time, but Kit successfully puts him off.
A little later, Kit runs into Nat Eaton, the captain’s son, at the docks. He's a bit grouchy because he has just delivered the fancy diamond-paned windows ordered for William Ashby’s new house and his Barbados bride. Nat, of course, assumes that Kit is getting married. The two exchange some heated words. That night, Nat and some of the men from the Dolphin decide to prank William Ashby by illuminating the windows of his new house with jack-o-lanterns. Nat and the men are put in the stocks for lighting the jack-o-lanterns and are banished from Wethersfield.
The novel’s political action starts heating up as Governor Andros comes to town to take Connecticut’s charter and replace it with his royal presence. The men in the town, among them Uncle Matthew, are livid and argue for their right to govern themselves (they are currently ruled by the King of England). Meetings take place at the Wood house and William Ashby, of all people, steals back the charter when Governor Andros visits. We also find out that John Holbrook has enlisted in the militia to fight the Indians.
Newsflash! A fever strikes the town’s young people. Kit and Judith get sick, as well as Mercy. Mercy has a terrible case of the fever, it turns out. The town looks for a scapegoat (someone to blame) and finds it in the Quaker Hannah Tupper. They decide she's a witch who has cursed the town with a fever. They form a mob to burn her house down.
Fortunately Kit gets to the Meadows in time to save Hannah. Hiding from the mob, Kit thankfully spots a ship in the river. It’s the Dolphin! Nat comes to the rescue and takes Hannah to his grandmother’s house. He offers to take Kit too, but she can’t leave, she tells him, because of Mercy.
Mercy’s fever finally breaks, but all is not well in Wethersfield. In the absence of Hannah, Kit is put on trial for being a witch. She is accused of consorting with the devil, mainly by Goodwife Cruff and her husband, who have found Kit’s hornbook (the little paddle she used to teach Prudence the alphabet) in the rubble of Hannah’s house – and their daughter Prudence’s name written on sheets of paper.
Though Uncle Matthew defends Kit, no one else in the town will help her – William Ashby doesn’t even show up to the examination. Fortunately, Nat returns from his banishment just in time to take little Prudence to trial to testify for Kit. With the young girl’s testimony (she proves that Kit was simply teaching her to read and write), Kit is set free. Nat must flee because of the banishment, but he tells Prudence to say goodbye to Kit for him.
Kit breaks off the engagement with William. (Finally!) Judith and William start to get cozy. John returns from the militia and runs into the waiting arms of Mercy. A double wedding takes place in which Judith and William marry alongside Mercy and John.
Kit concocts a plan to return to Barbados and become a governess, but before she does she realizes she’s in love with Nat. (Again: Finally!) Fortunately, Nat returns to Wethersfield, the proud owner of a ship named the Witch, and asks Kit to marry him. They plan to a future together that will include Hannah and both of their families.