Alexander VI refuses to allow a Catholic burial for Paolo, despite his doubts about the stable boy’s suicide, causing Lucrezia to embark on a hunger strike that threatens the life of her infant son; the French army heads back to Rome, allied with Sforza; Della Rovere slips back into the city unnoticed to launch a plot against the Pope’s life.

Cesare recruits a band of mercenaries with the help of Micheletto to seek revenge on the retreating French troops for burning the nunnery where his beloved Ursula lived; the Pope forges more strategic alliances and enriches himself in the bargain; Lucrezia joins Giulia's quest to aid Rome's poor.

Cesare deals with the cunning Sforzas decisively; Alexander disguises himself and travels to Florence to hear the fiery preacher Savonarola, not realizing that Della Rovere is trying to recruit the rebellious holy man to his cause.

Alexander is convinced that a lightning strike on St. Peter's Basilica during mass was a sign of God's disapproval; Cesare tries to prove his worth as a military commander; the Pope pressures the reluctant Lucrezia to enter another political marriage.

Juan's triumphant return from Spain is marred by his unsuccessful siege of the Sforza castle; Lucrezia purposely scuttles a scheme to marry her off to a rich Genovese merchant; Savonarola's forces conduct the infamous "Bonfire of the Vanities".

It's Easter and Alexander makes plans for a celebration to end his pious fast even as Della Rovere's assassin ascends to the position of the Pope's taster. Lucrezia's lover asks for her hand in marriage but her father dismisses him and his request. Juan's wild behavior threatens the life of Lucrezia's child, forcing Cesare to make a chilling decision about his brother.

Tragic news for the Borgia family is followed by a shocking revelation from Cesare; Lucrezia surprises herself by falling for a new suitor, Alfonso of Aragon, and accepts his proposal of marriage; Cesare tortures the rebel leader Savonarola but can't extract a confession, so he fakes one and burns the heretic; the assassin finally strikes with a poisoned chalice of wine.