Meanwhile, social unrest begins challenging the Roman rule of the city as Pagans and Christians come into conflict. When the Christians start defiling the statues of the pagan gods, the pagans, including Orestes and Hypatia’s father, ambush the Christians to squash their rising influence. However, in the ensuing battle, the pagans unexpectedly find themselves outnumbered by a large Christian mob. Hypatia’s father is gravely injured and Hypatia and the pagans take refuge in the Library of the Serapeum. The Christian siege of the library ends when an envoy of the Roman Emperor declares that the pagans are pardoned, however the Christians shall be allowed to enter the library and do with it what they please. Hypatia and the pagans flee, trying to save the most important scrolls, before the Christians overtake the library and destroy its contents. Davus chooses to join the Christian forces. He later returns with a gladius and starts sexually assaulting her, but quickly begins to sob offers his sword to her. However, she removes his slave collar and tells him he is free.
Several years later, Orestes, now converted to Christianity, is prefect of Alexandria. Hypatia continues to investigate the motions of the Sun, the Moon, the five known “wanderers” (planets) and the stars. Some Christians ridicule the thinking that the Earth is a sphere, by arguing that people far from the top would fall off the Earth. When they ask Davus his opinion he avoids conflict by saying that only God knows these things.
Hypatia also investigates the heliocentric model of the solar system proposed by Aristarchus of Samos; by having an object dropped from the mast of a moving ship she demonstrates to Orestes that a possible motion of the Earth would not affect the motion, relative to Earth, of a falling object on Earth. However, due to religious objections against heliocentrism, the Christians have now forbidden Hypatia to teach at the school. The Christians and the Jews come into conflict, committing violent acts against each other.
The leader of the Christians, Cyril (Sami Samir), views Hypatia as having too much influence over Orestes and stages a public ceremony intended to force Orestes to subjugate her. Hypatia’s former pupil, Synesius, now the Bishop of Cyrene, comes to her rescue as a religious authority counterweight, but says he cannot help her unless she accepts Christianity; she refuses. Hypatia makes a personal discovery, theorizing that the Earth orbits around the Sun in an elliptic, not circular, orbit with the Sun at one of the foci. Cyril convinces a mob of Christians that suades the mob otherwise, and they decide to stone her instead. When everyone goes outside to collect stones, Davus secretly suffocates her to spare her the pain of being stoned to death and tells the mob that she fainted. Davus leaves as they begin to stone her.