During the American Civil War in 1863, Amy, a 12-year-old student at the Miss Martha Farnsworth Seminary for Young Ladies in rural Mississippi, discovers a seriously wounded Union soldier, John McBurney. She brings him to the school's gated enclosure where the school headmistress, Martha Farnsworth, first insists on turning him over to Confederate troops, but then decides to restore him to health first. He is initially kept locked in the school's music room and kept under watch. Edwina, the schoolteacher who has had no experience with men, takes an immediate liking to John, as does Carol, a 17-year-old student who makes advances with an experienced air.
John begins to bond with each of the women in the house, including the slave Hallie. As he charms each of them, the sexually repressed atmosphere of the school becomes filled with jealousy and deceit, and the women begin to turn on one another. After Carol, who earlier made a welcomed pass at John, witnesses John kissing Edwina in the garden, she ties a blue rag to the school's entrance gate to alert the Confederate troops to the presence of a Yankee soldier. When a band of Confederate soldiers see it while passing the school, Martha lies and helps John pretend he is a relative loyal to the Confederacy.
Martha also becomes infatuated with John, and a flashback shows her having an incestuous relationship with her brother. Martha considers keeping John at the school as a handyman. She makes sexual advances toward him, which he resists.
Late one night, Edwina discovers John having sex with Carol in her bedroom. In a jealous rage, she beats him with a candlestick, causing him to fall down the staircase and break his leg severely. Martha insists he will die of gangrene unless they amputate his leg. The women carry him to the kitchen where they tie him to the table. Martha saws off his leg at the knee. When John awakens and learns that his leg has been amputated, he goes into a fury, convinced that Martha performed the operation as revenge for his rejection of her sexual advances.
John, again under lock and key, convinces Carol to unlock his door. He sneaks from his room into Martha's and steals a pistol and some personal items of Martha's including some letters from her brother. Convinced that Martha plans to hold him prisoner, John confronts Martha at gunpoint, claiming control of the house and declaring his intention to have his way with any of the women or girls. He gets drunk and then confronts the entire household, revealing that he read Martha's letters and that they implicate Martha and her brother in an incestuous relationship. In a fit of anger he also accidentally kills Amy's pet turtle, which he immediately regrets and apologizes for, to no avail, as Amy professes her hatred of him. Edwina follows John to his room and professes her love for him. They begin to kiss and it is later implied that they had sex.
Meanwhile, Martha convinces the others (except for Edwina, who is not present) that they need to kill John to prevent him from denouncing them to Union troops who have made camp within sight of the school. Martha asks Amy to pick mushrooms they can prepare "especially for him" and Amy says she knows just where to find some. At dinner, John apologizes for his actions, and Edwina reveals that she and John have made plans to leave the school and marry. John has been eating the mushrooms and the others pass the bowl without taking any except for Edwina. When she starts to eat some, Martha cries out for her to stop. John realizes he has been poisoned, leaves the dining room disoriented, and collapses in the hallway. The following day, the women sew his corpse into a burial shroud and carry him out of the gate to bury. They agree he died of exhaustion, and Amy denies she could ever pick a poisonous mushroom by mistake.
