Giordano Bruno is an ex-Dominican friar living in Elizabethan London as the guest of the French ambassador Michel de Castelnau. His special memory techniques and defence of Copernicus have brought accusations of witchcraft, and have led him to be excommunicated by the Catholic Church for heresy. Unknown to Castelnau, Bruno has been recruited by Queen Elizabeth’s spymaster Francis Walsingham to spy on the Catholics at the embassy.
Prophecy begins with a ritual: "cunning-man" Ned Kelley claims to converse with a spirit and describes a vision to his patron, the scholar and astrologer John Dee. Dee is convinced that the vision relates to an astronomical event due this year: the great conjunction of Jupiter and Saturn. Bruno is a little more sceptical. However, when Bruno is called away from his friend Philip Sidney’s wedding feast to inspect a dead body at the palace, the vision takes on a sinister significance. The Queen’s maid of honour, Cecily Ashe, has been murdered, and the sign of Jupiter has been cut into her breast.
Bruno has two allies at the embassy, Castelnau’s secretary Dumas, and the Scotsman William Fowler. But he also has a powerful enemy: Henry Howard, a nobleman from one of the most powerful Catholic families in England, has taken a strong dislike to him. Bruno infiltrates a ring of conspirators that includes the Scotsman Douglas, Castelnau’s wife, Henry’s nephew Philip Howard, and the messenger Throckmorton, who delivers secret correspondence to the imprisoned Mary Stuart (Mary, Queen of Scots). As they discuss plans to put Mary on the throne in place of Elizabeth, it becomes clear that some of them do not trust Bruno. Furthermore, Castelnau’s wife Marie is attempting to seduce Bruno and so keep him under her power. As he is drawn further into their intrigue, Bruno becomes convinced that he is being watched.
Meanwhile, Bruno decides to investigate the murder of Cecily Ashe. He befriends another maid of honour, Abigail Morley, who reveals that Cecily was secretly seeing a handsome nobleman. He gave Cecily gifts, including a signet ring, a perfume vial, and a mirror concealing a scrap of paper showing a particular date. Will this be the day of an assassination attempt? The signet ring bears the mark of Mary Stuart, and seems to be the ring mentioned in letters between Mary and Henry Howard; she had sent it to him but he never received it. How did it end up in the possession of Cecily Ashe?
Bruno and Dee test the perfume vial and find it to contain poison. Meanwhile Kelley has presented another vision: he describes a red-headed woman with the mark of Saturn on her breast, pierced by a sword and carried away by a torrent of water. Once again Kelley’s vision seems to come to pass when the red-headed girl Abigail Morley is found dead, a dagger through her heart and the sign of Saturn on her breast, tied to a post in the river. Dee is taken by Walsingham for questioning, and Kelley flees. When Bruno visits Dee’s house he finds drawings by Kelley that implicate him in a treasonous plot and exonerate Dee, but Bruno is attacked on the way to Walsingham’s house and the papers are stolen. That night, Dumas comes to Bruno and begins to confess to having taken the ring. But he is interrupted by Marie, who continues in her attempts to seduce Bruno.
During a dinner party at the Howards' house, Bruno seizes the chance to look for evidence against Henry Howard. He pretends to be so drunk that he has to stay the night, then creeps down to the library. He finds Henry Howard’s secret room, and papers proving Henry’s guilt in the conspiracy against Elizabeth. However, he is caught by Henry, and only escapes by climbing up the chimney and jumping into the Thames. He makes it home, but the papers are ruined by the water. At the embassy, another shock awaits him: Dumas has been murdered.
As the danger escalates around Bruno, villainy and treachery threaten both his own life and that of the Queen. From the College of Arms to a bear-pit in Southwark, Bruno searches for answers in a desperate quest to stay one step ahead of his unknown enemies and the distant power that ultimately drives all their actions.