อียิปต์ ศตวรรษที่ 4 ภายใต้การปกครองของอาณาจักรโรมัน... ความขัดแย้งทางศาสนาคุกรุ่นไปทั่วท้องถนนจนถึงห้องสมุดที่มีชื่อเสียงของเมืองอเล็กซานเดรีย นักดาราศาสตร์หญิงผู้ชาญฉลาด ไฮพาเทีย (ราเชล ไวซ์) และบรรดาสานุศิษย์ของเธอ ต้องต่อสู้เพื่อรักษาไว้ซึ่งภูมิปัญญาแห่งโลกโบราณ... ท่ามกลางเหล่าบุรุษผู้อยู่เคียงข้าง ไฮพาเทียเป็นที่หมายปองของสองชายผู้แก่งแย่งแข่งขันกันเพื่อเป็นเจ้าหัวใจของเธอ หนึ่งคือออเรสทิส (ออสการ์ ไอแซค) ผู้สูงศักดิ์ อีกหนึ่งคือเดวุส (แม็กซ์ มิงเกลลา) ทาสหนุ่มผู้ต้องเลือกระหว่างความรักและอิสรภาพ

The film centers around the astronomer-philosopher Hypatia of Alexandria (Weisz) and several men whom she knows such as her slave, Davus (Minghella), and her pupils, Orestes (Oscar Isaac) and Synesius (Rupert Evans), all of whom become major players in the changing political social landscape.[6] The film begins with Alexandria under Roman pagan rule. Hypatia, daughter of a scholar, teaches at the Platonic school, where many future leaders are educated. She is wooed by her student Orestes, while her slave Davus keeps his love for her secret. Meanwhile, social unrest begins challenging the Roman rule of the city as pagans and Christians come into conflict. The pagans, including Orestes and Hypatia's father, ambush the Christians to quash their rising influence, but find themselves unexpectedly outnumbered. Hypatia's father is gravely injured and Hypatia and the pagans take refuge in the Library of Alexandria. The Christian siege of the library ends when an envoy of the Roman Emperor declares that the Christians shall be allowed to enter the library. Hypatia and the pagans flee, grabbing what scrolls and documents they can, before the Christians overtake the library and destroy its contents. Davus, torn by his love for his mistress and the possibility of gaining his freedom by joining the rising tide of Christianity, chooses to join the Christian forces.

The film continues several years later: Hypatia has reluctantly married Orestes, who (now converted to Christianity) is prefect of Alexandria. Hypatia continues to investigate the motions of the heavenly bodies, though she is forbidden from teaching at the school. The Christians and the Jews come into conflict, committing violent acts against each other, with the Christians ultimately wresting power from the only other religious group remaining. 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. Cyril convinces a mob of Christians that Hypatia foments civil disobedience and they vow to kill her. Davus tries to run ahead to warn Hypatia, but she is captured by the mob. Davus secretly suffocates her while the mob gathers stone to stone her with.