Bethel is an isolated, theocratic patriarchy that follows a strict religious code called the Holy Protocol. The people worship the Father and submit to a male Prophet and his apostles. Bethel’s populace sits apart from the marginalized Outskirts, and the forbidden Darkwood encircles the land. The Darkwood harbors four powerful witches—Lilith, Delilah, Jael, and Mercy—who serve a rival deity called the Dark Mother.

Immanuelle attends the Sabbath service and receives a blood blessing from the Prophet along with her family but feels disconnected from the ceremony. Afterward, she relaxes by the river with her friend Leah, who will soon marry the Prophet. Immanuelle confides that, though nearly 17, she has not yet begun menstruation.

A group arrives that includes Ezra, the Prophet’s son, and Judith, the Prophet’s newest wife. Judith antagonizes Immanuelle about her mother’s past and her rumored lack of a spiritual Gift. Immanuelle deflects with a sarcastic remark about witchcraft, making Ezra laugh. He shares a lingering look with her before he departs.

At a tense Sabbath dinner, Abram Moore, Immanuelle’s grandfather and a disgraced former apostle, tells her to sell the family’s precious yearling ram, Judas. Immanuelle is painfully aware that her family’s poverty is the result of her mother Miriam’s crimes. Miriam had fallen in love with an Outskirter, the descendent of an impoverished tribe of refugees that Bethel had accepted centuries earlier. Despite this, Miriam was forced to marry the Prophet. Days later, she tried to kill the Prophet then fled into the Darkwoods. She emerged months later, pregnant, and the shame of her behavior cost Abram and his family everything. Immanuelle’s grandmother Martha warns her to avoid the Darkwood on her way to the market.

At the market, she lingers at a bookstall, where a shopkeeper pressures her to trade her mother’s necklace for a book. Ezra intervenes and shows Immanuelle a forbidden encyclopedia disguised to look like the Holy Scriptures. Disturbed by a girl punished in the stocks nearby, and afraid of breaking Holy Protocol, Immanuelle returns the book. Ezra slyly questions the morality of Bethel’s laws, shocking Immanuelle, and then departs.

Immanuelle fails to sell Judas and starts home as a storm breaks. The ram panics, catches her lip with a horn, and bolts into the Darkwood. Despite her grandmother’s warnings and years of horror stories about the Darkwood, Immanuelle follows him.

Immanuelle quickly loses her way but feels a strange calm and a pull deeper into the forest. She feels as if she is a part of the Darkwood and it is a part of her. Whispering voices guide her to a clearing where two naked with pale gray skin women lie entwined in a sexual embrace within a mushroom ring. Immanuelle is shocked by their nakedness and open sexuality. The women rise and fix their dead-white eyes on her.

One of the women presses a leather-bound book into Immanuelle’s hands. Compelled to accept it, Immanuelle tucks the book into her knapsack, then hears Judas cry out and runs toward the sound. She finds the ram’s severed head, recoils, and flees the wood.

She collapses at the forest’s edge, where Martha, her grandfather’s second wife Anna and Anna’s daughter Glory find her. Back home, Martha questions her about her decision to go into the wood. Immanuelle admits she lost Judas and saw two women in the Darkwood, but does not reveal the whole truth of what she saw. As punishment, Martha burns Immanuelle’s palm with a hot poker. Immanuelle promises to obey and keeps the book secret.

Alone, Immanuelle studies the book and realizes that is her mother’s journal. The journal reveals the truth of Miriam’s tortured affair with Daniel Lewis Ward, an Outskirter and Immanuelle’s father. In a series of increasingly manic diary entries, Miriam recounts how authorities forced her to watch Daniel’s execution by pyre, how grief consumed her after her marriage to the Prophet, and her mixed emotions when she discovered she was pregnant.

The journal contains frantic sketches that lead Immanuelle to identify the women she saw in the forest as Jael and Mercy, witches known as the lovers. The journal also includes sketches of Delilah, a water witch and Lilith, the antler-crowned witch queen. Immanuelle realizes that her mother knew these witches personally. The final pages of the journal repeat four words—Blood, Blight, Darkness, Slaughter—and end with a plea for help.

Eight days later, on the morning of Leah’s cutting ceremony, Immanuelle wakes from dreams of the witches. She decides to wear one of the only things she inherited from her mother, a red dress. Martha remarks that she looks just like Miriam. At the cathedral, Immanuelle confesses to Leah that she entered the Darkwood, and Leah makes her promise not to return. Immanuelle is overcome with grief at the idea that her friendship with Leah will be changing.

During the ceremony, the Prophet carves his holy seal into Leah’s forehead with a dagger, marking her as his wife. Bloodied but smiling, Leah sits up and licks the blood from her lips.

At the feast, Immanuelle notices that the Prophet is watching her. The Prophet orders the burning of effigies of Lilith, Delilah, Jael, and Mercy, the witches known as the Unholy Four. The crowd cheers as the effigies burn, disturbing Immanuelle, who retreats to the cemetery and vomits.

In the cemetery, Immanuelle witnesses a conversation between Judith and Ezra that suggests that they have had a physical affair. Ezra politely but firmly rejects her. In frustration, Judith grabs Ezra’s apostle’s dagger and snaps its chain. Ezra notices Immanuelle watching. She flees as a child screams near the bonfire.

That night, wails from the Darkwood draw Immanuelle from her bed. She follows the sound to a pond. A witch that Immanuelle immediately recognizes as Delilah emerges and takes Immanuelle’s branded hand, licks the burn, and leads her into the water. Delilah pulls her under, and Immanuelle sees visions of faces beneath the water. Suddenly, Immanuelle surfaces, and the witch is gone. Confused, Immanuelle swims to shore.

As Immanuelle approaches the shore, a witch appears wearing a deer skull and a crown of antlers. Immanuelle recognizes her as Lilith, also known as The Beast. When Lilith touches Immanuelle’s face, a sharp pain grips her, and blood runs down her leg—her first menstruation. As Lilith withdraws, Immanuelle staggers toward home but collapses.