On a remote island in Scotland's Loch Moidart, Eleanor Bruton, a covert operative of the Order of St. Katherine, lives alone, secretly studying a fragment of ancient embroidery depicting women's portraits, heraldic motifs, and foliage. Two young women break into her cottage, strike her, and steal the embroidery. Meanwhile, at Oxford University, a press release announces that 26-year-old PhD student Anya Brown has decoded Folio 9, a cryptic manuscript that defeated the world's finest minds.
Anya, the novel's central character, has impostor syndrome because her eidetic memory, the ability to recall everything she sees in perfect detail, feels like an unfair advantage. Her mother, Rose Brown, a book restorer who raised Anya alone after her father abandoned them, is undergoing chemotherapy but remains fiercely proud. Anya's boyfriend, Sid Hill, is finishing a computer science PhD at Oxford. Job offers pour in, but Anya cannot leave the country while Rose is ill.
Professor Diana Cornish of the Institute of Manuscript Studies at St. Andrews contacts Anya with an extraordinary offer: a generous salary, a rent-free cottage, and exclusive access to a private manuscript collection never before studied. Anya's Oxford supervisor, Professor Alice Trevelyan, encourages her to pursue it. After visiting St. Andrews, Anya is taken to a remote castle where she meets Tracy Lock, a famous actress who vanished from public life and the keeper of the private manuscript collection, and sees manuscripts of exceptional quality. Anya and Sid accept the offer.
What Anya does not know is that Diana belongs to the Fellowship of the Larks, a centuries-old secret society of women who believe in shattering the glass ceiling. The Institute is staffed by Lark members and serves as a front for their search for The Book of Wonder, an extremely valuable hidden manuscript. Their rivals, the Order of St. Katherine (the Kats), pursue the same goal but believe women should exercise influence through traditional roles as wives and mothers. The two groups have clashed violently for centuries. Eleanor's death was the Larks' work; the embroidery and clues encoded in a manuscript collection, they believe, together reveal the book's location.
In London, Detective Constable Clio Spicer of Scotland Yard's Art and Antiques Squad attends the retirement party of her mentor, Detective Sergeant Lillian Shapiro. Lillian reveals a decades-long secret investigation into the two groups and connects them to a 1968 British Museum theft in which a fragment of medieval embroidery, known as the Everly Binding, was torn in two. The smaller piece remains on display; the larger piece vanished. Lillian asks Clio to investigate Eleanor's death quietly. Days later, Lillian is killed by a hit-and-run car outside the museum under suspicious circumstances. Clio suspects murder and begins investigating alone. She rents Eleanor's cottage and discovers a poem sewn into a curtain hem, signed with a symbol later understood as a St. Katherine's wheel, containing cryptic references to Verona, Italy.
After settling in St. Andrews, Anya is taken to London to meet the true benefactor behind the manuscripts. In a mews house in Belgravia, she discovers the benefactor is Magnus Beaufort, her estranged father, a wealthy physician and philanthropist building a grand library in Cambridge. Diana reveals that the core of Magnus's famous collection, believed destroyed in a fire 25 years earlier, survived: About 200 of the finest volumes were moved before the blaze. Anya initially refuses to work with Magnus but strikes a deal: She will study the manuscripts if he gets Rose accepted onto a US clinical trial without Rose ever knowing he is involved. Magnus delivers, and Rose calls with the joyful news.
Meanwhile, Sid receives an anonymous note about Minxu Peng, a Chinese woman who had worked at the Institute and previously lived in their cottage before disappearing. His research reveals that Institute staff have backgrounds in finance rather than medieval studies, that Diana and Trevelyan studied together at Oxford, and that a dark web post claims Folio 9 was forged by Trevelyan to draw Anya in. Paul Fields, the partner of Anya's colleague Giulia Orlando, confides that another woman also vanished from the Institute and that he fears the staff are responsible.
Diana is murdered by a Lark assassin after her secret affair with a judge and her botched cover-up of Minxu's death make her a liability. Her corpse is staged with St. Katherine symbolism to implicate the Kats. Charlotte Craven, the Larks' senior leader, realizes too late that Diana had the stolen embroidery fragment sewn into her bra. Clio later discovers the fragment while inspecting Diana's personal effects, photographs it, and replaces it.
Rose, sharp despite her illness, calls Anya and reveals a devastating secret: Years ago, a legendary bookbinder named Josephine Dunne entrusted Rose with a glossary that is the key to deciphering the Voynich manuscript, one of the world's most famous untranslatable texts. The Voynich encodes the location of The Book of Wonder. Rose hid the glossary inside the binding of a bestiary, a medieval book of animals, in Magnus's collection, then set fire to his library to destroy it, but the bestiary had been moved before the blaze. She tells Anya to find it and run.
Anya identifies the bestiary by Rose's coded description of a black panther illustration and smuggles it out of the castle. That night, Sid discovers Paul Fields's body in the cathedral ruins, an apparent suicide. They flee St. Andrews by car. In an Edinburgh hotel, Anya extracts the glossary and a Latin letter from the binding. The letter, written by Isotta Nogarola, a 15th-century feminist scholar from Verona, reveals that Isotta, three of her sisters, and their aunt created the Voynich using a private family language, encoding within it the location of The Book of Wonder, hidden to protect it from men.
Anya and Sid fly to Verona, where Clio tracks them down. The three join forces, connecting the embroidery portraits to the five Nogarola women and linking Voynich imagery to Verona's medieval architecture. When Anya learns that her mother's carer, Viv, is a Kat operative who has abducted Rose, the urgency intensifies. Viv also claims Folio 9 was forged, though Anya cannot confirm this.
Using the glossary and star symbols on the embroidery as a cipher, Anya decodes the Voynich's final paragraph to spell "Hypogeum Santa Maria Assunta," identifying an underground Roman complex beneath a church near the Nogarola family's country villa. She slips away before dawn and descends alone into dark tunnels, finding painted chambers whose ceilings mirror the Voynich's most mysterious imagery. Pursued through a flooded passage, she escapes up a well shaft into a room adjoining the church. Inside, she finds an ancient chest bearing the Nogarola crest, opens a hidden compartment, and extracts The Book of Wonder.
Magnus's men seize her but release her abruptly after a phone call frightens them away. When the carabinieri, Italy's national police, arrive, Anya hands over the bestiary as a decoy, keeping The Book of Wonder concealed in her backpack.
Anya arranges a meeting at a café in Verona's Piazza Isotta Nogarola. Tracy Lock arrives for the Larks; Cece Beaufort, Magnus's wife, arrives for the Kats, revealing that the two most powerful women in Anya's father's life belong to opposing secret societies. Anya sets her conditions: Rose returned safely, her clinical trial honored, and Clio's safety guaranteed. The Kats will keep the book, and Cece will donate its equivalent value to fund the Lark Foundation, the Larks' planned public organization to support women. A breaking news alert confirms Magnus has died in a helicopter crash near St. Andrews, an "accident" the two groups engineered to remove him and seal their agreement. They offer Anya continued work on the collection, proposing to rename the library after Rose.
Anya speaks to Rose by phone, confirming she is safe. Sid hands the book to Tracy, and both women depart. Meanwhile, Clio reviews museum CCTV footage and, with help from her colleague DC Izzy Adefope, identifies the wife of Tony Axford, Izzy's superior and the detective who had pulled Izzy off the Diana Cornish murder investigation, among those who surveilled Clio and Lillian during their earlier museum visit. Izzy suggests the younger woman beside her may be the new wife of Tim Keenan, Clio's supervisor at the Art and Antiques Squad. Both wear St. Katherine's wheel imagery, confirming corruption within the police force. Clio resolves to expose it.
Walking along the river, Anya reflects on whether either group truly helps women or merely seeks power. She concludes, gazing at the ancient city, that the women of both organizations "did what it took" (290). She will never feel fully safe again, but she has secured her mother's life and reclaimed some control over her own.