Sergeant Neil Howie of the West Highlands Constabulary receives a photograph and an anonymous letter reporting the disappearance of a 12-year-old girl, Rowan Morrison, on nearby Summerisle. Resolving to investigate, he travels to the private island in his sea-plane. On landing, the harbour-master insists that Howie seeks permission from Lord Summerisle. The islanders on the shore do not recognise Rowan from Howie's photograph, but direct him to May Morrison's post office. There he meets May's actual daughter Myrtle, but when he asks her about Rowan, the girl will only say that Rowan is a hare who plays in the fields.
At The Green Man inn, landlord Alder MacGregor offers Howie a room and asks his daughter Willow to look after the policeman. While the locals sing laciviously about Willow's charms, Howie examines some harvest festival photographs and notes that the previous year's photograph is missing. Willow gives Howie a supper of canned food and, when he asks for one of Summerisle's famous apples, tells him they have all been exported. That night outside his window, Howie sees Lord Summerisle presenting a young boy to Willow for sexual initiation. He tries to pray but is distracted by the sound of noisy sexual intercourse.
The next morning, Howie visits the island's school. The children claim not to know Rowan, but Howie finds her name in the register and accuses them of being liars. Taking him outside, the schoolmistress explains that Rowan's soul has returned to nature and that the children only learn of Christianity as a comparative religion. By a ruined kirk, he finds what is apparently Rowan's grave, adorned with her umbilical cord. From the island's doctor, Howie learns that Rowan burnt to death, but can find no entry for her at the records office.
Howie visits Lord Summerisle, who grants him permission to exhume Rowan's body. When the policeman expresses disgust at a fertility ritual being performed in the grounds, Summerisle explains that his agronomist grandfather bought the island for its soil and climate, in order to grow new strains of fruit. By way of motivating the islanders, he reintroduced them to the Old Gods of nature and fertility, and soon the island's apple harvest made it prosperous.
Howie returns to the kirk and opens Rowan's grave, but finds only the body of a hare. He accuses Summerisle and the islanders of murder, threatening to return the next day with more police from the mainland. Howie breaks into the chemist's and discovers the previous year's harvest festival photograph, which depicts Rowan Morrison and Summerisle's failed crop. He speculates that she may not be dead, and will be sacrificed at the May Day celebrations the next day. That night, Willow sings to Howie through his bedroom wall and Howie presses up against it, tormented.
The next day, Howie finds his sea-plane will not start and is told he cannot return to the mainland for over a week. He researches fertility rituals and processions at the library, as the islanders prepare their costumes. Howie conducts a fruitless door-to-door search for Rowan, eventually returning to The Green Man to rest. After avoiding an attempt to drug him, Howie attacks MacGregor and steals his Punch costume.
As the procession begins, Summerisle teases MacGregor (really the disguised Howie) for his poor dancing. There is a mock execution by swordsmen of an islander dressed as a hare. Eventually the procession arrives at the shore and Summerisle offers a sacrifice of ale to the gods of the sea. Howie spots Rowan dressed in white and grabs her. They escape into a cave, emerging on the cliff-top, only to be greeted by Summerisle and the islanders. Howie realises he has been tricked. Summerisle explains that he, not Rowan, is the perfect sacrifice, having come of his own free will, with the power of the king; a virgin and a fool. Howie appeals to the islanders, insisting that his death will not save their crops, but he is stripped, anointed, and placed screaming inside a huge, hollow wicker effigy of a man atop the cliffs. As he prays, the pyre is lit and the islanders begin to sing.
