Set in the summer of 1964, the novel opens in Neshoba County, Mississippi, where a group of white men, including Olen Leonard and his cousin Sheriff Bickford, arrive at a wooded clearing to find three civil rights workers, two white and one Black, shot dead in a shallow grave. One man photographs the bodies while others collect body parts as souvenirs. The scene establishes the violent racism of Jim Crow Mississippi and the complicity of law enforcement in racial terror.
The story shifts to Violet Richards, a 21-year-old Black woman in Jackson, Mississippi. Her older sister Rose drowned eight years earlier in an accident Violet blames herself for. Their father died of a heart attack a few years later, and their mother had a fatal stroke the previous fall, leaving only Violet and her 22-year-old sister Marigold. One night, walking home from a bar, Violet is raped by a white man named Huxley Broadus. When she and Marigold report the assault, the police dismiss the claim. After Huxley begins stalking her, Violet kills him with her father's pistol and hides the body. Knowing that a Black woman in Mississippi will never receive justice, she decides to flee.
Violet meets Dewey Leonard, Olen's white son, who believes they are eloping to marry up north. Violet does not love him; she has cultivated the relationship as an escape plan. When a police officer pulls them over in Alabama, Dewey claims Violet is his family's maid. At dawn in Birmingham, Violet steals Dewey's wallet while he enters a restaurant, runs to the Greyhound station, and boards a bus to Washington, DC.
Back in Jackson, Marigold wakes to morning sickness. She is about two months pregnant by James Scott, a New York lawyer working on the Mississippi Summer Project, a civil rights voter registration campaign. She finds Violet's room empty with a note saying Violet has "messed up" and is leaving. When Marigold tells James about the pregnancy, he flees Jackson overnight, claiming a family emergency. Police come looking for Violet, and a newspaper reports that Huxley Broadus has been found shot dead, with Violet sought for questioning.
Roger Bonny, Marigold's boyfriend of two years, argues that the police may pin the murder on Marigold if they cannot find Violet. He proposes they marry and move to Cleveland, Ohio, where his brother Frankie works at a steel mill. Pregnant, abandoned by James, and fearing arrest, Marigold accepts. Meanwhile, Dewey hires Mercer Buggs, a white man desperate for money to pay medical bills for his son Randy, who has rheumatic fever. Mercer negotiates a fee of $2,500 to locate Violet, with instructions not to harm her.
On the bus, Violet impulsively gets off in Chillicothe, a tiny Georgia town where her cousin Birdie Mae Hudson lives. She adopts the alias "Vera Henderson." Lilly Dukes, a local girl, guides Violet to Birdie's house and then to a boardinghouse run by Willadene Mason, known as Miss Willa. Needing work, Violet takes a job as maid for Bettyjean Coogler but discovers that Bettyjean's husband is Sheriff Butch Coogler. The sheriff's persistent questions about Violet's background convince her the job is too dangerous. She quits and is hired as a cook at the Starlight Diner by John Palmer, a white owner who refuses to segregate his restaurant. Bettyjean retaliates by falsely accusing Violet of theft, and Palmer fires Violet rather than cross the sheriff.
Hank Cummings, a 26-year-old Black farmer who owns 25 acres inherited through generations from a slaveholder ancestor, has been courting Violet. Drawn to his confidence and honesty, she eventually moves to his farmhouse. Meanwhile, Lilly arrives at the boardinghouse beaten by her father, a local pastor who threw her out after discovering she is attracted to women. After Lilly reveals she drank turpentine to end a pregnancy, Violet vows to help women facing similar situations.
After visiting the Richards house in Jackson posing as a lawyer, Mercer tracks Marigold and Roger to Cleveland, where he confirms Violet is not with them. In Cleveland, Roger refuses to find steady work, pursuing a nightclub fantasy, and he slaps Marigold after an argument. Mercer approaches Roger at a bar, introduces himself as "Dewey Leonard" from Florida, and poses as a nightclub investor, cultivating the relationship to learn Violet's whereabouts. When Mercer follows Marigold home from a library and tries her locked apartment door, she recognizes him as the man who visited her Jackson house and calls Violet to warn her.
Examining Dewey's wallet more carefully, Violet discovers a photograph of the three dead civil rights workers in their shallow grave, with Olen Leonard visible in the background. Unable to approach the Federal Bureau of Investigation (FBI) because of Violet's legal jeopardy, the sisters hide the wallet. After Roger hits Marigold again, kicking her in the stomach, Lurlene, Frankie's wife, drives Marigold to the bus station. Marigold boards a bus to Chillicothe without telling Roger her destination. In Cleveland, a drunken Roger tells Mercer that Marigold has gone to visit her sister near Augusta, Georgia. Mercer now knows where Violet is. He calls not Dewey but Olen Leonard, revealing that Dewey has been pursuing a Black woman. Olen orders Mercer to kill Violet for $10,000, demanding photographic proof and threatening Mercer's wife if he fails. Mercer drives to Georgia with a gun, a gas can, and a camera.
In Chillicothe, Violet throws a fish fry so Marigold can meet her friends. Marigold privately reveals the baby's father is the Summer Project lawyer and that she has left Roger. That night, Marigold begins to miscarry, and a midwife confirms she is losing the baby. After white teenagers harass Violet and Hank at the roadside stand, the Ku Klux Klan burns a cross in Hank's yard. The threat convinces Violet to stop running: She agrees to marry Hank, and he secretly drafts a will leaving the farm to her.
While Hank demolishes the old sell shed to pour a new foundation, a vehicle strikes and kills him. Sheriff Coogler dismisses the sole witness's description and leaves without investigating. That night, Mercer approaches the darkened farmhouse with his gun, but Dewey appears behind him and shoots him dead. Dewey has followed Mercer to Georgia after his father boasted about ordering the hit. Breaking into the house, Dewey takes Marigold hostage and demands his wallet. He admits to killing Roger in Cleveland and Hank earlier that day. He explains that the photograph was his leverage to turn his father and the Citizens' Council, a white supremacist organization, over to the FBI once he and Violet were safely up north. Violet pretends she still cares for Dewey, persuades him to release Marigold, retrieves Hank's shotgun from the hall closet, and shoots him.
Before sunrise, the sisters bury Dewey and Mercer in the hole Hank dug for the foundation and pour concrete over the grave. They burn the photograph and wallet. The community fills the church for Hank's funeral, where Violet wears the cream organza wedding dress she had bought for their ceremony. A lawyer reveals Hank's will, leaving the farm to Violet. Marigold learns from a former colleague that the FBI is rounding up Neshoba County suspects, including Olen Leonard, and that Dewey and Mercer are listed as fugitives. Lurlene reports that Roger was found shot dead in Cleveland; police seek someone named "Dewey Leonard from Florida." Marigold keeps silent.
Marigold boards a Greyhound to Washington, DC, planning to find work, enroll in college, and attend law school. Violet settles into running the farm with Hank's workers and her community. She acknowledges that law enforcement may one day uncover her identity but resolves to stop running, having found freedom and belonging not through flight but through staying rooted in the land Hank left her.