The novel opens in 1628 in the village of Batchcombe, Wessex, where a young woman named Bess Hawksmith flees her prison cell in chains. She runs toward Batchcombe Woods, where Gideon Masters, a dangerous warlock who has long pursued her, waits with horses. Bess refuses his offer and races toward the sea cliffs, pursued by hounds and villagers. At sunrise, she steps from the cliff's edge into the void. A brief passage then establishes the narrator as Elizabeth Anne Hawksmith, aged 384, beginning a new Book of Shadows, a witch's journal of spells and personal history.
In February 2007, Elizabeth moves into Willow Cottage in the English village of Matravers. She appears roughly fifty, tall and strong, with long auburn hair marked by a snow-white streak from her magical transformation centuries ago. She lives alone, sells herbal products at a nearby market, and stays alert for a pursuer who has followed her through the centuries. Tegan, a lonely teenage girl recently relocated to the village with her mother, Helen, begins visiting the cottage. Elizabeth is drawn to the girl, who reminds her of her long-dead sister Margaret. When Tegan bluntly accuses Elizabeth of being a witch, Elizabeth decides to share her history, framing the story of Bess Hawksmith as a tale about a distant ancestor.
The narrative shifts to 1627. Fifteen-year-old Bess works the hay harvest with her family: her father John, her mother Anne (a skilled herbalist and healer), her brother Thomas, and her younger sister Margaret. Bess yearns for adventure beyond Batchcombe. William Gould, the quiet son of the local squire, is infatuated with her. Meanwhile, Bess is disturbed by Gideon Masters, a charcoal maker who lives as a recluse in the woods. While gathering moss, she witnesses Gideon sexually assaulting a bound Romani girl. When he confronts Bess afterward, she refuses to be intimidated, and he notes that her mind is unusually resistant to his influence.
That autumn, the plague strikes Batchcombe. Thomas, Margaret, and John all die within days. When Bess herself falls gravely ill, Anne goes to Gideon and begs him to save her daughter at any price. Gideon performs a dark ritual. The magic enters Anne, and she uses it to cure Bess, though Anne's hair turns white overnight and something fundamental in her changes. Bess recovers unmarked, but Anne refuses to reveal the price she paid. She eventually confesses the truth: She became a witch to save Bess's life.
The witchfinder Nathaniel Kilpeck arrives in Batchcombe, sent by Parliament to root out witchcraft. Neighbors accuse Anne and Old Mary, the village midwife, of cursing their children with the plague. During a two-night "watching," a vigil designed to reveal a witch's familiars, hideous imp-like creatures emerge and fawn upon Anne, confirming the accusation. Anne and Old Mary are sentenced to hang. In jail, Anne makes Bess promise to go to Gideon for protection. Anne is hanged from the Hanging Tree. Bess watches without tears, honoring her mother's wish.
Bess goes to Gideon's cottage as promised. He instructs her in magic, and she becomes drawn to him despite knowing what he is. One night, she discovers him presiding over a satanic ritual, his face transforming into a bestial, goat-like creature. He tells her he has asked Satan to bless her transformation; she refuses, saying she would rather die. Kilpeck's men arrest Bess the next morning, and she is quickly convicted. In jail the night before her execution, she speaks the incantation Gideon taught her and screams his name. Power surges through her, snapping her chains, and she escapes through the iron bars. Court records claim she flew from the cliff at Batchcombe Point, connecting this escape to the novel's opening scene.
In the present, Elizabeth instructs Tegan in hedge witchcraft, the benign practice of healing and working with nature. She then tells Tegan the story of her life as Eliza in 1888 London, where she works as assistant to the surgeon Dr. Phileas Gimmel at the Fitzroy Hospital while running an evening clinic for prostitutes in Whitechapel. A visiting Italian medical researcher named Signor Damon Gresseti, introduced to the Fitzroy by Dr. Gimmel as a guest from the Milan Institute of Medical Research, unsettles Eliza with his presence. She also grows close to Abigail Astredge, a frail patient with an undiagnosed wasting illness, and develops feelings for Abigail's devoted brother, Simon Astredge.
Prostitutes from Eliza's clinic begin turning up murdered in the killings attributed to Jack the Ripper. Eliza notices unsettling signs of a hidden presence: the melody "Greensleeves" recurs around her in inexplicable ways, played by an organ grinder who denies having the tune and by a music box in Abigail's room. Eliza rearranges the letters of "Damon Gresseti" and discovers the name is an anagram of "Gideon Masters." She confronts him on the night of Samhain (Halloween), and Gideon stands revealed, but Mary Jane Kelly is murdered that same night, leaving Eliza uncertain whether she defeated him. She then realizes "Simon Astredge" is also an anagram. During surgery on Abigail, the patient opens her eyes, revealing herself as Gideon's willing accomplice. Gideon drops the Simon disguise, kills the surgical assistants, and blinds Dr. Gimmel. Eliza transforms into a butterfly and escapes through a window.
Back in the present, Elizabeth formally initiates Tegan into the craft during a moonlit ceremony. Tegan's boyfriend, Ian, an appealing man in his late twenties who lives on a narrowboat, visits Willow Cottage, and Elizabeth feels overwhelming terror in his presence. When Tegan's mobile phone rings with "Greensleeves," the melody that has signaled Gideon's presence across centuries, Elizabeth is certain: Ian is Gideon.
For the first time, Elizabeth resolves not to flee. Her love for Tegan gives her a reason to fight. She reveals her true identity to Tegan and shows Tegan Ian's demonic nature through a reflecting pool. To prepare Tegan, Elizabeth tells a final story: her time as Elise, a nurse at Passchendaele during World War I. There, she uses her magic openly, guiding the spirit of a dying soldier to the Summerlands, a peaceful afterlife. She falls deeply in love with Lieutenant Archie Carmichael, a Scottish officer who senses her power and accepts her completely. Gideon, disguised as Lieutenant Maidstone, lures Elise to an abandoned schoolhouse. Archie bursts in to rescue her, and when Gideon prepares to kill Elise, Archie throws himself in front of the fatal blast. He dies instantly, though his shot wounds Gideon, who escapes as a raven.
Elizabeth and Tegan spend weeks preparing for a confrontation on All Hallows' Eve. Elizabeth plans to draw Gideon to Batchcombe Woods, where their story began, on Samhain, when the veil between worlds is thinnest. On Halloween night, Tegan lures Gideon to the woods. Elizabeth appears in full power, glowing and levitating. The battle is fierce: Elizabeth commands the trees to march toward Gideon; he blasts them back. He sends swarms of bats against Tegan; Elizabeth summons owls to destroy them. Sister witches arrive, whirling around the clearing, but Gideon fights them off. He seizes Elizabeth by the throat until Tegan strikes him with a rock. Gideon retaliates by blasting Tegan's shoulder with magical fire, leaving a permanent scar, then brings Elizabeth crashing to the ground.
From the earth, the spirit of Anne Hawksmith rises, summoned from the Summerlands. Anne wakes her daughter and pours strength back into her. Restored, Elizabeth approaches Gideon and offers him her hand, asking if he truly wishes to be with her. His pride causes him to agree. Elizabeth reveals the trap: Because he has come willingly, the sister witches and Anne can escort him to the Summerlands, where he will cause no harm. He screams but cannot break free. Elizabeth mouths "Be strong" to Tegan and vanishes with Gideon, her mother, and the witches in a flash of light.
Tegan, alone in the burning woods, walks to Willow Cottage, which Elizabeth has left to her in a will. Writing the final entry in the Book of Shadows, Tegan notes that the Summerlands is not permanent and that Elizabeth promised to return. She resolves to continue studying the craft and be ready.