In AD 391, Alexandria is part of the Roman Empire, and Greek philosopher Hypatia is a teacher at the Platonic school, where future leaders are educated. Hypatia is the daughter of Theon, the director of the Musaeum of Alexandria. Hypatia, her father's slave, Davus, and two of her pupils, Orestes and Synesius, are immersed in the changing political and social landscape. Orestes tries to woo Hypatia with music, but she rejects Orestes's love by showing him her menstrual rags, because she prefers to devote herself to science. Davus assists Hypatia in her classes and is interested in science. He is also secretly in love with her. Meanwhile, social unrest begins challenging the Roman rule of the city as Pagans and Christians come into conflict. When the Christians start verbally insulting the statues of the pagan gods, the pagans, including Orestes and Theon, ambush the Christians. However, in the ensuing battle, the pagans unexpectedly find themselves outnumbered by a large Christian mob. Theon 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 Theodosius I declares that the pagans are pardoned, but the Christians shall be allowed to take possession of the library. Hypatia and the pagans flee while 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 sexually assaults Hypatia, but he begins to sob and offers his sword to her. However, she removes his slave collar and tells him that he is free. Several years later, Orestes, now converted to Christianity, is prefect (Roman state official serving as governor) of Egypt. 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 what his opinion is, 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, which demonstrates 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 violent conflict. The leader of the Christians, Cyril, 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 theorizes that the Earth orbits around the Sun in an elliptical orbit, not a circular orbit, with the Sun at one of the foci. Cyril convinces a mob of Christians that Hypatia is a witch, and they vow to kill her. Davus tries to warn Hypatia, but she is captured. They strip Hypatia and are about to skin her alive until Davus persuades the mob otherwise, and they decide to stone her instead. When the mob goes outside to collect stones, Davus suffocates her to spare her the pain of being stoned and tells the mob that she fainted. Davus leaves as they begin to stone her.

A Kurdish family is trying to survive after the death of its parents. Ayoub, the eldest boy in the family, becomes the head of the household and must do whatever work available to survive. Madi, Ayoub's handicapped brother, is in need of surgery. Ayoub goes to great lengths to collect money for the surgery. He becomes a kolbar and smuggles truck tires with a group of Kurdish villagers near the Iran-Iraq border. Ayoub ultimately falls short of his intended goal and his uncle decides to marry off his sister in return for the groom's family financing Madi's surgery on the Iraqi side of the border. When they arrive the mother of the groom refuses to accept Madi and agrees to give Ayoub and his uncle a mule as compensation. Ayoub decides to take the mule to Iraq, where it is worth more, and sell it to pay for his brother's surgery. Some smugglers let him come along with him. They use mules to carry goods and feed them whisky, allowing them to better survive the harsh mountain winter. However, they are ambushed while heading to the border, and the mules are too drunk to carry on. Ayoub narrowly manages to escape, and the last shot is of him and his brother crossing the border.

Dieter and Margot Menliff, in an unhappy marriage, visit an old castle that Margot has just inherited. When they arrive, Dieter explores the basement, while Margot examines the rest of the castle. Dieter sees something in the cellar that causes him to drop his keys and flee. Margot has a vision in a dusty mirror. Halfway through the film, a second couple, Eva Ziehnagel and Gregor Grause, is introduced.