In Rome, Marcus Junius Brutus arrives home, and is somewhat put out to receive only a perfunctory welcome from his mother, Servilia, after his long absence.
Caesar and his Legion arrives in Alexandria in pursuit of Pompey, who sought refuge with his "friends" in Egypt. Caesar is greeted by the ministers of the young King Ptolemy XIII. When Caesar refers to the dispute over the throne between Ptolemy and his sister/wife, Cleopatra VII, Ptolemy's regent, the eunuch Pothinus makes light of the situation, claiming it has affected Egypt little: however, in private, Posca informs Caesar that the Egyptians are lying, and that the situation is far worse. Caesar is also clearly irked by the petulant and childish king.
At the urging of his tutor Theodotus, young Ptolemy presents Caesar with a large jar containing Pompey's head, in an attempt to placate Caesar and bring him to their side in the conflict with Cleopatra. Instead, Caesar is outraged and disgusted by their barbaric murder of "a consul of Rome." As recompense for this insult, Caesar demands two things: the life of Pompey's assassin, and full repayment of the debt owed to Rome by the King's late father, in the amount of "seventeen thousand thousand drachma," an amount entirely impossible for the Egyptians to pay, given the "minor" unrest caused in the countryside by Cleopatra's dispute.
Caesar decides to remain in Egypt to arbitrate between the various factions, ordering Mark Antony to return to Rome, despite Antony's and Posca's warnings that he will be left with dangerously few men in Egypt, surrounded by hostile factions that could make him into a common enemy, and that Cato the Younger and Scipio are still at large and likely gathering fresh forces.
Vorenus and Pullo are dispatched to the south of the country to find Cleopatra and escort her to Alexandra. Meanwhile, Pothinus and Theodotus persuade Ptolemy to anticipate Caesar's decision by having his sister killed, while she is still under house arrest. They also decide to temporarily placate Caesar by delivering Pompey's assassin, Septimius, asking him to deliver a message to Caesar, in person, which turns out to be his own death warrant. A short time later, Septimius's head is placed on a stake outside the palace.
Vorenus and Pullo wait for Ptolemy's assassins to appear, to guide them to Cleopatra's exact location. When the assassins arrive, the Romans ambush them just as they are about to kill Cleopatra.
As her litter travels to Alexandria, Cleopatra confides in her servant, Charmian, that it is imperative that she seduce Caesar. "If I cannot, then I am dead." She notes that, if she could bear him a son, something his three wives have not done, her position would be much more secure. She also notes that it will be several more days before they reach Alexandria, but now is the perfect time for her to become pregnant, as her "womb is between the flood." To this end, she orders Charmian to invite Vorenus into her tent and orders him to have sex with her. Though tempted, Vorenus refuses and storms out of the tent, instead ordering Pullo to "[r]eport immediately to Princess Cleopatra and do as she says." Confused, Pullo reports for duty, but when he learns what his task is to be, he performs it with gusto. Afterwards, Vorenus warns him never to speak of it, as Caesar will likely have him killed if he finds out.
Vorenus and Pullo smuggle Cleopatra into Alexandria concealed in a sack. The moment she reveals herself, Caesar is immediately smitten with her. She enters the throne room, where her younger brother quails before her. Sweetly, she tells him she does not blame him, but that he has been manipulated by his evil advisers and swiftly demands their deaths. Shortly thereafter, Pothinus and Theodotus's heads join Septimius's on the stakes outside the palace. Angered by this sign of Roman imperialism, a mob begins gathering outside the palance, and Vorenus orders his men to bar the gates and prepare for combat.
Cleopatra swiftly seduces Caesar into making an alliance, sealed by enticing him to have sex with her. Scenes of Cleopatra and Caesar making love are interspersed with scenes of Servilia and Octavia in bed, and scenes of the mob laying siege to the palace.
Almost a year later, in Rome, Cicero meets Brutus in the Senate House. Cicero says that, if Caesar is defeated in Alexandria, then they should do everything possible to keep Antony from assuming power after him. Brutus reminds him that they swore loyalty to Caesar when they surrendered, but Cicero parries that their oath does not extend to Antony. Antony then enters, telling Cicero that he's heard rumors of Cicero's planned treachery, and warns him that, if he ever hears of it again, he will cut off Cicero's "soft, pink hands and nail them to the Senate door." As he is leaving, Antony adds that he came with good news: Caesar is victorious in Alexandria.
In Alexandria, we see Ptolemy floating facedown in the river, dead. Caesar presents Cleopatra's infant son Caesarion to his soldiers. As the Legion cheers, Vorenus glowers at Pullo, who pauses for a moment, knowing that there's a distinct possibility that the child is his, then goes on cheering proudly.