Ann Lee, Amanda Seyfried, is born in Manchester in 1736. As a child she and her younger brother William Lee, Lewis Pullman, toil in a cotton factory. One night she witnesses her parents in a sexual act and interprets it as sin; during a family meal she declares she knows what her father does to her mother, and her father responds with a harsh switch to her hands. As she grows, she becomes more devout and takes a job as a cook at a local infirmary. One day she, William, and their niece Nancy visit the home of Jane Wardly, Stacy Martin, and James Wardley, Scott Handy, Quakers who preach that Jesus’s Second Coming will be a woman and embrace public confession of sin and impromptu shouting, dance, and song as part of worship. Ann becomes a fixture within this group of “shaking Quakers” and marries fellow believer Abraham Standerin, Christopher Abbott.
Ann’s trepidations around sex are worsened by her husband’s interest in sadomasochism and oral sex, and the tragedy of all four of their children dying in infancy; her brother William is described as a latent homosexual. As the Shakers grow more provocative in their practices, they unsettle locals and disturb the peace enough that authorities arrest Ann and imprison her for 14 days, during which she refuses to eat or drink. She has a vision of levitation and of Adam and Eve in the Garden of Eden, which she takes to mean that original sin was fornication and therefore humanity must abstain from marriage and sex; the Shaker leaders rename her “Mother Ann.”
After an angry crowd injures Ann and her followers, they choose to depart Britain for New England, funded by John Hocknell, David Cale, a wealthy farmer. They sail aboard the Mariah, where Nancy becomes enamored with the new convert Richard, Hocknell’s son. Despite their rituals being mocked by the crew, Ann helps keep up morale during a violent storm and earns their respect. Upon arriving in New York City, Ann sends William and other men north to find land for their community. During the months waiting to hear back, Nancy leaves the community to marry Richard and Abraham leaves Ann, frustrated with their marriage and lack of sex.
That spring, Ann and the others rejoin William in Niskayuna, where they have begun developing a settlement, guided by a vision Hocknell has, including his finger-wagging and pointing him to the meadowland site. William is sent out to preach at other established communities. The population of Niskayuna steadily grows with converts and foundling children who are adopted into the community. Ann is arrested by the Continental Army for insisting their community remain neutral during the war. After being freed by the sympathetic governor, she travels around New England, establishing Shaker communities, though some people suspect her of witchcraft.
Ann recruits new followers at a local farm where they are attacked by an angry mob. The farm is burned down and several Shakers are beaten and killed. Ann, though telling the Shakers not to resist, is stripped naked below the waist by men who question her gender and accuse her of witchcraft. Badly injured, Ann recalls her childhood with William during their journey home. William dies shortly after, and prominent follower Mary Partington, Thomasin McKenzie, is half-blinded. A year later, Ann, who never recovered from the attack, dies as well and is buried in the village which is now a thriving and self-sustaining religious community. The credits mention the population of various Shaker communities, and that there are only two Shakers left in 2025.