The first novel in C. J. Sansom's Shardlake series is set in England in November 1537, during the reign of Henry VIII. Thomas Cromwell, the king's chief minister, is orchestrating the dissolution of England's monasteries, seizing their wealth for the Crown. Cromwell summons Matthew Shardlake, a hunchbacked lawyer and committed reformer in Cromwell's service, to Westminster. He reveals that Robin Singleton, a commissioner sent to pressure the Benedictine monastery of St. Donatus the Ascendant at Scarnsea into surrender, has been found beheaded in the monastery kitchen. A report also describes the desecration of the church and the theft of a prized relic. Cromwell insists the crime must be solved quickly and secretly, lest it embolden resistance to dissolution across England. He appoints Shardlake to the case and orders him to bring Mark Poer, a young man in his household. Mark, the son of Shardlake's father's steward, recently lost his position at the Court of Augmentations, the government office managing dissolved monastic property, after a sexual liaison with a lady-in-waiting.
Shardlake and Mark ride south through bitter cold and arrive at the monastery, a sprawling Norman complex bordered by marshland. Shardlake meets the key figures: Abbot Fabian, determined to resist surrender; Prior Mortimus, a harsh Scottish disciplinarian; Brother Edwig, the stammering bursar; Brother Gabriel, the tormented sacrist responsible for the church; and Brother Guy of Malton, the infirmarian, originally from Moorish Granada. Brother Jerome, a monk of the stricter Carthusian order and a distant relative of the late Queen Jane Seymour, also lives in the precinct. Jerome was tortured on the rack until he swore the oath of supremacy, recognizing the king as head of the Church, and the experience has left his mind unhinged. He confronts Shardlake upon arrival, quoting Scripture menacingly. At the infirmary, Shardlake meets Alice Fewterer, Brother Guy's young assistant, whose composure and directness immediately interest him.
Shardlake examines Singleton's body and deduces that the killer used a sharp sword and struck with practiced skill. The kitchen is normally accessible only to a few keyholders. A young novice, Simon Whelplay, collapses from exhaustion at supper after enduring Prior Mortimus's punishments. At the same meal, Jerome makes a treasonous outburst declaring the Antichrist has come. That night, feverish and delirious, Whelplay tells Shardlake that Singleton was not the first to be killed and tries to warn Alice of danger, but he is too ill to explain. The next day, after visits from four senior monks, Whelplay goes violently mad and dies. Brother Guy determines he was poisoned with the toxin belladonna. Shardlake realizes the boy was killed to prevent him from revealing what he knew.
Alice tells Shardlake that the account book Singleton was studying before his death has not been included among those delivered to his room. When questioned, Jerome tells a chilling story: In the Tower of London, he heard Mark Smeaton, the court musician falsely accused of adultery with Queen Anne Boleyn, weeping the night before his execution and insisting Cromwell had racked him into confessing. Jerome calls Singleton a perjurer and swears he knows of no man in the monastery who could have committed the murder, a qualification whose significance Shardlake does not yet grasp.
Shardlake sends Mark into the frozen fish pond to retrieve a gleam of yellow he spotted earlier. Mark finds a gilt-handled sword and then disturbs a decomposed female body. Fair hair and a silver pendant suggest the body is that of Orphan Stonegarden, a foundling who worked as the infirmarian's assistant and was reported to have stolen gold cups and fled. Her neck is broken. A monk's habit bearing the sacrist's badge, stained with apparent blood, is also found. Shardlake accuses Gabriel, but laundry records confirm the robe was reported stolen weeks before the murder. Gabriel later confesses to a different secret: He bored a spyhole in a hidden passage behind the infirmary to watch visitors undressing. This passage, discovered by Mark, also connects to the kitchen corridor, meaning the kitchen was not as secure as Shardlake believed. Moments later in the church, Gabriel shoves Shardlake aside as a stone statue is pushed from a walkway above. The statue crushes Gabriel to death; he dies saving Shardlake's life. The attacker escapes.
Shardlake sails to London to report to Cromwell and investigate the sword. The Tower armorer identifies it as the work of John Smeaton, Mark Smeaton's father. Cromwell casually confirms that the charges against Anne Boleyn were entirely fabricated and that Singleton was assigned to torture young Smeaton into a false confession. Shardlake is devastated: His belief that Cromwell's methods served a greater moral purpose collapses. Tower records show a young woman visited Smeaton's cell the night before his death. At the elder Smeaton's house, Shardlake learns the sword was inherited by the dead man's sister.
Back at Scarnsea, Shardlake orders Brother Edwig arrested after the bursar makes a treasonous outburst at supper, but Edwig vanishes. A messenger from London confirms the identity of Smeaton's visitor. Shardlake finds Alice packing to flee and arrests her for Singleton's murder. Alice confesses: Mark Smeaton was her cousin and her lover, and her mother was John Smeaton's sister. She stole Gabriel's habit, entered the kitchen through the hidden passage, beheaded Singleton with her uncle's sword, and desecrated the altar with a sacrificed cockerel to make the killing look like the work of outsiders. Mark Poer suddenly appears with a dagger at Shardlake's throat. He and Alice became lovers during Shardlake's absence in London, and he has known her secret since then. They plan to escape across the flooded marsh to a smuggler's boat. Shardlake warns them the marsh is impassable, but they bind and gag him and leave.
Brother Guy finds Shardlake the next morning. At the rear gate, two sets of footprints lead into the floodwater, and Shardlake presumes Mark and Alice drowned. Jerome is found hiding in the plinth where the relic stood; he stole it after the murder to prevent its destruction. Following dropped gold coins, Shardlake finds Edwig in the bell tower with heavy panniers of gold from hidden land sales. Edwig confesses: Tormented by guilt after killing Orphan Stonegarden in a fit of lust, he planned to smuggle the gold to the Catholic Church in France to buy divine forgiveness. He killed Whelplay to keep the secret and tried to kill Shardlake by pushing the statue in the church. In the struggle, Shardlake is knocked over the railing and clings to a bell to save himself. Edwig tries to flee, but the heavy panniers tip him over the edge, and he falls to his death.
Three months later, Shardlake returns to supervise the monastery's dissolution. The buildings are being stripped bare. Abbot Fabian has lost his wits, and Jerome died in prison. Brother Guy, refused permission to leave England, plans to go to London, where Shardlake offers to help him. Guy gives Shardlake a letter smuggled from France: Written in Mark's hand but from Alice, it reveals that she and Mark survived the marsh, reached the boat, married, and are living quietly abroad. Alice expresses no regret for killing Singleton. Shardlake stands at the marsh's edge with Brother Guy, confessing his grief and love for Mark and Alice, as the sounds of demolition echo from the dying monastery.