In 1630 New England, a devout Puritan named William is banished from a colonial plantation along with his wife Katherine and their children: Thomasin, Caleb, fraternal twins Mercy and Jonas, and newborn baby Samuel. The family travels to the edge of an isolated forest to build a solitary farm.

Tragedy strikes quickly when Thomasin plays peekaboo with Samuel near the edge of the woods. In a split second, the infant vanishes without a trace. A witch living deep in the forest has stolen the baby, killing him to use his fat for an unholy flying ointment. Katherine falls into deep grief and religious mania, constantly praying and blaming Thomasin for the loss.

As their crops rot and winter approaches, William and Caleb hunt secretly in the forest. Caleb encounters a sinister cottage and falls under the spell of an alluring woman in red. He returns to the farm naked, sick, and possessed. During an agonized prayer session in the house, Caleb spits out a bloody apple slice, professes his love for Christ, and dies.

The twins accuse Thomasin of witchcraft, claiming their black goat, Black Phillip, speaks to them. In turn, Thomasin points out the twins' disturbing behavior. Desperate, William locks Thomasin and the twins inside the goat barn overnight. Later that night, a monstrous figure infiltrates the barn and attacks the children.

By morning, the barn is destroyed, the twins and goats are gone, and William is fatally gored by Black Phillip. Katherine attacks Thomasin in a mad rage, forcing Thomasin to kill her mother in self defense. Left entirely alone among the corpses of her family, Thomasin walks into the barn to confront Black Phillip.

The goat speaks in a smooth human voice, asking her if she wants to "live deliciously." Defeated by her pious, repressive upbringing, Thomasin signs her name in Satan's black book. She strips off her clothes, walks into the woods, and joins a coven of levitating witches around a roaring fire, finally bursting into euphoric, terrified laughter.

The ending reveals that the supernatural threat was real all along. Black Phillip is an avatar of the Devil, who preyed on the family's extreme isolation and dogmatic shame. Thomasin did not start as a witch, but every institution meant to protect her - family, church, and society - rejected and condemned her. With no home, no kin, and only starvation or the gallows waiting for her, she accepts Satan's offer of freedom, luxury, and power. Her final flight above the trees represents a dark liberation from Puritan bondage.