In November 1347, seventeen-year-old Eleanore (Elea) Blanchet lives in Avignon, the seat of the papacy in southern France, with her twin sister Margot, their father Bernard (a papal notary), and their housekeeper Anes. Elea is an herbalist trained by her mother, Bietriz, a gifted midwife who died in childbirth two years earlier. Bietriz's death was compounded by cruelty: Mathilde Dupont, a former friend, spread rumors that Bietriz was a witch, so no physician would help her, and the parish priest, Father Loup, refused to administer last rites.
Margot is engaged to Erec Dupont, Mathilde's son. While gathering herbs outside the city, Elea frees a feral dog from a poacher's trap, using an intuitive gift for communicating with animals. When Erec asks Elea to treat his ailing mother, she reluctantly agrees and discovers that Mathilde's physician has left a bloodletting wound badly infected. She sutures it using her mother's surgical tools. Walking home, Elea encounters a procession of flagellants, penitents who publicly whip themselves to atone for sins. Their leader is Father Loup, supposedly exiled but now preaching apocalyptic hatred. The next day, after papal guards drive the flagellants out, Elea visits the dog and names him Baldoin.
On a later outing, Elea meets Guy de Chauliac (Guigo), the most famous physician in Christendom and personal doctor to Pope Clement VI. Impressed by her herbal knowledge, he invites her to his laboratory in the papal palace. After her tincture relieves the pope's symptoms, Elea strikes a bargain: if she can examine Clement and diagnose his ailment, Guigo must take her as his apprentice. She identifies a swollen kidney and prescribes a tonic from her mother's book. When the pope improves, Guigo honors the deal.
Elea's education begins in earnest as she accompanies Guigo on rounds through hospitals and almshouses and studies anatomy through dissection. Meanwhile, Erec's father is murdered and the family business proves bankrupt. Erec tells Margot he cannot marry her, leaving her heartbroken.
A letter reaches Clement from Marseille: plague-bearing ships have docked and a catastrophic pestilence is killing hundreds daily. Two strains are described: a pneumonic form spread through breath and a bubonic form marked by swollen tumors called buboes. Guigo and Elea research historical plagues but find no cure. The plague's first victim in Avignon dies despite every effort. Guigo's friend Dr. Jacob Farissol, a Jewish physician, brings his nephew and apprentice, David Farissol, to help. David survived the plague in Marseille after his entire family died, and he and Elea share an immediate connection.
Avignon descends into catastrophe as twenty thousand perish. Elea moves into the palace laboratory, and she and Guigo try every remedy they can devise, but nothing saves a single pneumonic plague victim. Guigo persuades Clement to lift the church's ban on human dissection. The pope orders Father Loup, now reinstated as priest of Saint-Agricol, a parish church in Avignon, to supply corpses from La Pignotte, the parish poorhouse. At La Pignotte, Father Loup recognizes Elea and calls her a witch. Guigo fiercely defends her, and Elea tells him the full story of her mother's death. Guigo assures Elea their gifts come from God.
Queen Joanna of Naples arrives for her murder trial, visibly pregnant, and the court exonerates her. Because all midwives in Avignon are dead or fled, Elea is summoned to serve as the queen's midwife. She also befriends Paolo di Rosa, a Florentine musician in Joanna's court. When the bubonic plague reaches the city, Guigo and Elea dissect victims and theorize that lancing the buboes before blood poisoning sets in might save lives. One afternoon, Elea recognizes a corpse on the dissection table by her own suture work: It is Mathilde Dupont. Shaken, she presses forward, remembering a tonic for blood poisoning from her mother's book.
David contracts the bubonic plague, and Guigo performs the dangerous lancing surgery. David survives. During daily bandage changes, an undeniable attraction develops between Elea and David, though both know that as a Christian and a Jew, any relationship carries a death sentence. Elea's father then contracts the pneumonic plague, for which no surgery exists, and dies at dawn.
When Joanna goes into labor a month early, Elea discovers the baby is positioned the wrong way with the cord wrapped around her neck, the same complication that killed Elea's stillborn brother. Using a technique she watched Bietriz attempt, Elea turns the child and delivers her alive. Then Guigo falls ill with bubonic plague, and Elea performs the surgery alone for the first time. It succeeds.
As Guigo recovers, anti-Jewish violence escalates. Father Loup incites mobs blaming Jews for the plague, and Elea spots Erec cheering beside the priest. She warns David, and they share their first embrace. David asks Elea to flee with him to Granada, a kingdom in southern Iberia where Christians, Muslims, and Jews live freely together. She declines, unable to leave Margot and Guigo. After witnessing Erec in the mob, Elea burns an undelivered letter Margot wrote begging Erec to marry her. When Joanna prepares to leave Avignon, she offers Elea a permanent position in Naples, but Elea declines, receiving generous payment and a royal title.
The morning after Joanna's departure, a young man lures Elea from the laboratory by claiming Margot is ill. He is a confederate of Father Loup's. Elea fights back but is overpowered. That evening, Father Loup drags her before a crowd, accusing her of witchcraft and conspiring with Jews, brandishing her drawings and her mother's book as evidence. Erec pushes through the crowd, shouting that Elea is no witch and that he was promised she would not be harmed, but monks overpower him. Father Loup condemns Elea to burn at dawn.
In her cell, Elea makes peace with death. She dreams of the ruined cottage in the woods, now whole and lit, where her parents and baby brother wait. Her mother meets her eyes through the window but gently closes it. That night, Paolo and a sympathetic monk unlock her cell. Erec found Guigo, who organized the rescue despite his weakened state. Outside the church, hooded figures wait: Anes, Erec, Guigo, and a fourth person Elea does not identify. She tells Erec to take care of her sister and rides east with Paolo.
The next morning, Elea is seized by the sensation of being burned alive and collapses screaming. Throughout their lives, Elea and Margot have shared a psychic bond as twins, and what Elea feels is her sister's death. Paolo tells the truth: Margot contracted the pneumonic plague and, knowing she was dying, insisted on taking Elea's place on the pyre so Father Loup would not burn another innocent. Guigo carried Margot to the cell dressed in Elea's clothes. The fourth hooded figure was Margot herself, saying a silent goodbye. In the pocket of an embroidered cloak Margot made for her, Elea finds a note in her sister's handwriting: "You are myself."
In the epilogue, Elea stands on the deck of a ship bound for Valencia and then Granada. She carries a letter from Guigo hoping she will return when the plague passes. David appears beside her, having settled his aunt and uncle in Marseille. Baldoin, who found Elea on the road, paces the deck at their feet. Elea takes David's hand, honoring Margot's final wish: "If you have another chance for happiness, take it." The novel closes with lines from Dante's
Inferno: "Where we came forth, and once more saw the stars."