As the Tiber flows past the Castel Sant’Angelo, we hear the screams of a prisoner in its bowels. Micheletto walks in to offer Girolamo Savonarola a chance to end his days of suffering and sign the confession but Savonarola laughs as he ruins it with ink. In the Vatican, The Pope demands of Cesare either a confession from the heretic Savonarola or his brother, Juan. Cesare passes on this command to the Captain of the Guard; Cardinal Sforza says to add mortuaries to the list of places to search.
A retinue of wagons arrives in Rome, its occupants throwing gold to the chasing children. Lucrezia encounters the strangers in a hallway and becomes acquainted with her latest suitor – Prince Alfonso d’Aragona, Duke of Bisceglie and Prince of Salerno. He does not recognize her and she grasps the opportunity to have a little fun with him. Under the guise of taking him to ‘her lady Lucrezia’, she leads him to her apartments and shares a playful back-and-forth.
In a small chapel, Antonello meets with della Rovere and explains his failed attempt to assassinate the Pope. But della Rovere explains they will not be deterred and he will know when it is time to strike. Back in the dungeons, Savonarola taunts Micheletto by calling him a sodomite. Micheletto is not shaken and Savonarola says he will only confess to Cesare. Lucrezia and Alfonso d’Aragona walk in the gardens together, under a large parasol, and Lucrezia continues her charade with him. He subtly proposes they become lovers if ‘her lady’ accepts his betrothal, which Lucrezia refuses. He then says he will eschew the betrothal altogether, if she will run off with him because he has never known a lady so sweet. Lucrezia expresses pity for him feeling that way, gives him a small kiss and dashes off, leaving him holding the oversize parasol.
That afternoon, Machiavelli is a guest of Cesare’s and they discuss the difficulty of extracting a confession from Savonarola. Cesare knows that a confession is needed to recant all that was preached but Savonarola has proven stronger than he thought over the lengthy torture. Cesare states that Rome needs that confession; Machiavelli states what he thinks to be obvious: then give it to them. Rodrigo is visiting with Lucrezia and his grandson and mentions that a new suitor, Alfonso d’Aragona, has finally arrived to court her. Lucrezia smiles knowingly and plays along, stating she will dutifully meet with him. She again plays the diva and keeps everyone waiting for her arrival. She is played in by bell chimes and a choir and leaves her suitor dumbfounded by the discovery of her true identity. She declares immediately that she will marry him and the Pope is elated. However, while leaving the Captain of the Guard stops Cardinal Sforza to relate they have found a body. The Pope goes outside to the trailer only to find that it is the wrong man. When the Pope asks if his son ordered this, Cardinal Sforza admits he believes Juan to be dead and they have been searching the mortuaries on his command. Pope Alexander then takes it upon himself to search the mortuaries, escorted by Giulia Farnese. In the meantime, Cesare sits across from Savonarola demanding he sign the confession. Savonarola admits he is tired and broken and even passes out for a moment but he awakes and says that God speaks to him. Cesare takes this as an admission and signs the confession in Savonarola’s name. He admonishes Micheletto the prisoner must never speak of this and storms out. Savonarola screams he will use his last strength to curse the Pope and shout to the world the falseness of the confession. Micheletto cuts out his tongue.
Giulia and Rodrigo search a mortuary and are shown the bodies from the river. Rodrigo finds Juan and tells Giulia to take him home. Cesare is triumphantly making his way to the Pope but walks in to find a gathering of his family and cardinals over Juan’s corpse. The Pope laments how he was found and wonders aloud who would do such a thing. Lucrezia not so quietly states that one of the many people he harmed could have done it. The Pope demands she repeat herself and she launches into a defiant tirade about the many people who could have done it, what he'd done to her and how she was not sorry he was dead. The Pope asks why Cesare has shed no tears; Cesare states he is out of tears and gives his reasons. The Pope banishes them from his sight. Giulia and Vanozza bear witness to this with not a tear shed between them. Later in his bedroom, Rodrigo bemoans to Vanozza why he did not see the rift in his own family. Vanozza tells him he saw with a father’s eyes and admits she was not fond of Juan either. When she suggests arranging the funeral, Rodrigo vehemently refuses.
Savonarola is carted to the platform leading to his heretic’s pyre. Citizens of Rome have turned out to heckle and throw rocks but the Pope is absent from his dais. Micheletto straps Savonarola in place and hangs the 'hereticus' sign about his neck. Cesare must bring the Pope from Juan’s mourning chamber to witness the burning. The Pope stops the lighting of the fire and walks out to Savonarola. He offers him one last chance to repent; Savonarola spits in his face. The fire is lit and Girolamo Savonarola burns to death.
Lucrezia and Cesare lounge together in her bed, lovingly holding hands. Lucrezia asks if Cesare will marry her and he plays on the words to tease her. He says as she wishes, they shall have to run away together, change their names and live in a fishing village on the coast. Of course, he knows what she truly means and states that he cannot. He says his hands have seen too much of blood and sin. When Lucrezia states his hands wear a cardinal’s ring, he says that they may no longer and leaves her.
Cesare looks for his father and finds him still in the mourning chamber. The Pope has not eaten and sadly recounts how he has fasted, scourged himself and abstained yet God continues to punish him. He vows he will not rest until Juan’s killer is found. Cesare tells him there will be no need, he knows who killed Juan. When the Pope says “Tell us!”, Cesare asks, “You truly wish to know?” Something comes over Pope Alexander and he sits down, stating he must know. But Cesare has conditions for this knowledge: first the Pope must hear his confession, release him from his cardinal’s vows and grant forgiveness for his sins. Cesare recounts his accomplishments and states they have all been for Rome, the church and his father. As he kneels at his father’s side, he states: “… I have taken upon my head the act that none other would dare commit though its commission benefits all. I swore a vow long ago that I would put an end to anyone that brought dishonor upon our family, dishonor on Rome, dishonor on you.” With that, the Pope comes to the realization that Cesare has killed Juan. The Pope is stricken but finds the words to release Cesare from his vows. Cesare removes his cardinal’s ring, places it upon Juan’s chest and leaves Pope Alexander forlorn.
Cesare seeks out Vanozza and Lucrezia to tell them that Juan’s funeral has been arranged. Vanozza reminds Cesare that his father will not have it and Cesare states firmly that it is done. He also insists that Lucrezia’s betrothal festivities take place and Vanozza is outraged. In the ballroom, surrounded by well-wishers, Cesare brings Lucrezia and Alfonso’s hands together to signify their betrothal and the festivities begin. The Pope sits in the darkened mourning chamber while below the ballroom is filled with dancing and music. He rises and crosses to Juan’s body, removing his papal rings. He lifts Juan into his arms and the corpse of the grown man is changed to body of a sleeping child. Rodrigo nuzzles him and carries him out of the Vatican to a patch of garden. He places him gently on the ground, says a small prayer and begins to dig, with his bare hands and a shovel. Meanwhile, Vanozza looks on intently as her two remaining children dance together closely, also watched by Alfonso. When Rodrigo finishes the shallow grave, the corpse of Juan as a man is present and Rodrigo drags him into the ground and covers him. He says another small prayer and leaves.
Lucrezia and Alfonso are leading another dance when Vanozza confronts Cesare about his motives for moving forward with the festivities. She states they are dancing on his brother’s grave. Rodrigo interrupts the party by showing up in the ballroom with his papal vestments covered in dirt and mud, asking to speak with Cesare. They sit at a table together, and though he has been alone most of the time, Antonello makes an appearance to serve the Pope’s wine. He drinks a large portion first and approves it for the Pope’s consumption. The Pope’s cup is poured and Antonello steps aside. The Pope does not drink immediately because Cesare asks what happened to Rodrigo’s hands. He states he has buried Juan. He takes a sip of his wine and shares that he realizes he has brought everything upon himself. That everything that has happened was his own doing. He tells Cesare he favored Juan because it was so easy. He sees now he made Cesare who he was because Cesare was too much like himself and he could not bring himself to favor him. Cesare asks for forgiveness if he cannot have affection but before the Pope can speak he begins to sputter and choke. Cesare looks to see Antonello bleeding from his eyes and coughing up blood. Cesare jumps up and runs to the boy but it is too late for him. He turns his attention to the Pope who is now beginning to convulse and bleed from the mouth. At first, he waves Cesare off but then grabs onto him as he collapses and Cesare bellows for help. The Pope is seizing on the ground as cardinals and his family rush into the room calling for him. Cesare cradles his father’s head, staring into his face in disbelief and then raises his head to the sky.