The narrator, Mary Katherine Blackwood (known as Merricat) introduces herself and reveals that all of her relatives are dead, except for her sister Constance. She then begins her story some time earlier, on the day she brought home the library books that still sit on her shelf, long overdue.
It’s Merricat’s job to go into town for groceries, but she doesn’t like having to face the villagers, who are hostile towards her. The Blackwoods’ land is closed off from the outside world with a fence, and the villagers have always hated the Blackwood family. Merricat hates the villagers in return and often wishes them dead. When she enters the grocery store, everyone goes silent until the owners have helped her and she leaves.
On her way home, Merricat goes into Stella’s café to show that she isn’t afraid. Jim Donell follows her inside to pester her, insisting he’s heard that she and her sister are moving away, which Merricat denies. Joe Dunham comes in, too, and Merricat has to endure their sly insults until Stella tells her to go home. On the way home, the Harris boys chant a rhyme at her about Constance poisoning her with a cup of tea.
Merricat returns home, where Constance welcomes her and begins making lunch while their Uncle Julian looks over his papers, which detail the death of the rest of the family six years earlier. Then they prepare for tea, as an old family friend named Helen Clarke is coming to visit. It becomes clear the Constance isn’t used to interacting with people other than Merricat and Uncle Julian.
When Helen Clarke arrives, Merricat greets her and finds that she’s brought her friend Mrs. Wright. Over tea, Helen Clarke urges Constance to reenter the world, and Constance’s openness to this idea worries Merricat, so she smashes a pitcher in the kitchen.
Uncle Julian comes into the drawing room and begins to discuss the night that the rest of the family was poisoned with arsenic at their dinner. Julian himself also ate the arsenic, but in a small enough quantity that he survived, though it has affected his memory. Mrs. Wright can’t help showing her fascination with this topic, despite Helen Clarke’s disapproval. Julian details the reasons why Constance might have been guilty or might have been innocent. She was tried for murder but acquitted. Constance and Merricat enjoy his performance, and eventually Helen Clarke forces Mrs. Wright out the door.
The next day, Merricat senses that a change is coming in their lives, so she chooses three magic words that will prevent it coming until the words are said aloud. Uncle Julian’s health seems bad that day, and after Dr. Levy comes to examine him, the sisters and Uncle Julian sit in the garden and talk about the day of the poisoning. Uncle Julian reveals that he and his wife felt that the sisters’ father resented the financial burden of their presence in the household.
On Sunday, Merricat and her cat, Jonas, wander the property. Merricat checks on various items that she has buried as magical protection for the house. She finds that a book she nailed to a tree has fallen, and she takes it as a terrible omen. After lunch, Merricat sees a man coming up the steps of the house. She thinks he’s one of the many people who come to try to gawk at Constance and take souvenirs from the house because they’ve heard about the poisoning. However, Constance lets the man into the kitchen and introduces him as their cousin, Charles Blackwood. Merricat is upset that she has let him in, so she spends the night in her hiding place by the creek with Jonas.
The next morning, Merricat returns to the house. Though she says that Charles was a ghost, Constance insists that he spent the night in their father’s bed, which is proved when Charles comes downstairs and meets Uncle Julian. He tries to make friends with Merricat, but she refuses to speak to him. Uncle Julian wants to write about Charles’s perspective on the trial, but Charles doesn’t want to talk about it.
While Merricat and Constance clean the house, Charles tries to get closer to Merricat through Jonas, and Merricat plots how to get rid of Charles. She eats dinner with the family because Constance wants her to. At dinner, Charles offers to take over the job of getting groceries in town, and Constance is grateful to him.
The next day when Charles goes into town, Merricat takes her father’s gold watch chain out of Charles’s room and nails it to a tree. When Charles finds it, he’s enraged that she would damage something so valuable. He threatens Merricat while Constance is out of the room.
Under Charles’s influence, Constance begins to think that she has done wrong by keeping the family isolated from the world. Merricat asks Charles to leave, but he refuses, so she breaks the mirror in his room. Uncle Julian has also begun to mistrust Charles, and he hides his papers in a box.
On Thursday, while Charles tries to fix the back step, Merricat tries to wipe out Charles’s mark on the house. She breaks her father’s watch, which Charles has claimed, and fills his room with wood and dirt. Meanwhile, Charles digs up the silver dollars she’s buried in the woods. She cleans out her shelter by the stream to get rid of his influence, and when she returns home, Charles is furious about the state of his room. He wants to punish her and is exasperated by Uncle Julian’s delusions—it becomes clear that Julian believes Merricat died during Constance’s trial. Eventually Merricat runs away and goes to the deserted summerhouse, where she imagines her dead family showering her with words of praise and indulgence.
When Merricat returns to the house, Constance, Charles, and Uncle Julian are eating dinner. Merricat goes upstairs and tips Charles’s burning pipe into the trash can, then joins them at the dinner table. Before long, Charles smells smoke and discovers that his room is on fire. He runs for help while Uncle Julian goes to collect his papers. Merricat and Constance shelter on the porch, hidden behind some vines. Firemen arrive along with a crowd of villagers, who would like to see the house burn down. Charles is most concerned about getting the safe out. Once the fire is out, Jim Donell, the chief fireman, throws a rock through the drawing room window, spurring the villagers to storm the house and begin destroying it from inside.
Merricat and Constance try to run to the woods, but the villagers surround them, taunting them. They only stop when Dr. Levy and Jim Clarke announce that Uncle Julian is dead. Merricat takes Constance to her shelter by the stream, where they acknowledge for the first time that Merricat poisoned their family.
When Merricat wakes up the next morning, she knows that everything will be different from now on. She and Constance discover that only the ground floor of their house is left. The kitchen is littered with broken china, glass, and furniture, but Constance manages to make breakfast anyway. When they eventually get up the courage to look at the rest of the house, they find that the drawing room and the dining room are both a mess. Merricat shutters these rooms and they close the doors forever. They clean the kitchen and the front hall, and lock the front door.
Before long, Helen and Jim Clarke turn up at the door, calling for the sisters and claiming that they want to help. Merricat and Constance hide, and eventually the Clarkes leave. Merricat covers the kitchen windows with cardboard so no one can see in. Later, Jim Clarke returns with Dr. Levy, who wants to make sure they’re not hurt. Merricat and Constance sit at the table behind the covered windows until the men leave. Constance apologizes for the night before when she reminded Merricat why their family died and she promises she’ll never bring it up again.
Over time, the sisters create a new pattern for their life. Merricat always makes sure the front door is locked, and she barricades the sides of the house with junk to prevent people from getting into the garden. People use the path through their front yard now, and sometimes children play on the lawn. Constance wears Uncle Julian’s old clothes, and Merricat wears tablecloths. They plant a rosebush on the spot where Uncle Julian used to sit in the garden.
The villagers begin to leave food on the porch in the evenings with notes apologizing for various items they broke the night of the fire. Merricat never strays past the garden anymore, and she and Constance often sit at the front door and watch the people outside. One day, Charles arrives with another man, who says he’ll pay Charles for a picture of him with one of the sisters if he can get them to come out. Charles begs Constance to let him in, but she doesn’t. The moment he leaves they both laugh uproariously at his foolishness.
The people who walk past the house always speculate about the sisters, and children are afraid of them. There’s a rumor that the sisters eat children, and Merricat and Constance joke about it. They feel they have little to fear anymore, and they are happy.