Hypatia (the criminally luminous Rachel Weisz), privileged daughter of Theon (Michael Lonsdale), is a crack mathematician and astronomer who refers to herself as a "philosopher." The parlance of the time, perhaps, but it doubles as a feint: In an increasingly intolerant religious atmosphere, questioning the mysteries of the stars is considered blasphemous. Hypatia is cosseted by her father and the adoring group of students she teaches at the famous Alexandria library, perhaps because she seems to be the only female within the city limits. (Seriously: where do they keep them?) Though there are some Jews kicking around, most of Alexandria is Pagan, a faith of Greco-Roman extraction that Amenábar implicitly attaches to enlightenment and civilization, despite the fact that its elite has a pesky attachment to their slaves. This conflation presents the film's first narrative speed bump: The intrepid Christians challenging the establishment are defiantly anti-Pagan, but the initial conflict is not well defined. The sympathetic weight Amenábar places on the physical destruction of Pagan idols feels confused; is Paganism just another blood-soaked religion or the faith of choice for knowledge-seeking progressives?
Amenabár's take on the founding Christians, however, is clear: Though he briefly references the then-revolutionary concept of Christian charity, the faith is portrayed mainly as a haven for radical ideology. Shortly after Ammonius persuades Hypatia's slave Davus (Max Minghella) to give his master's bread to the poor, he is leading a mob of black-hooded marauders to destroy the library. The books don't burn -- they are scrolls, in fact -- but the point is clear. In one of a series of directorial oversells (he belabors both wonky low angles and ground-sweeping aerial shots), Amenábar follows the hail of scrolls as they fly up to the ceiling like streamers, then turns the frame fully upside down. Although the preceding battle scene is a riveting evocation of panic, confusion and utter brutality, its import is unclear: Are we meant to side with science or the Pagans? Is the one being made indistinguishable from the other for the purposes of narrative expedition?
Having overthrown the Pagans, the Christians come calling for the Jews, and a holy war again breaks out in Alexandria's streets. A new Bishop (Sami Samir) with a bible-thumping bent turns his wrath definitively on heathens who would dare to question the word of God on the creation and the orbit of the earth; astronomers unlucky enough to also be women were doubly cursed. In the film's second act Amenábar draws a clear and chilling portrait of the divisive lines humans have felt compelled to lay down throughout history, the destructive instinct to define ourselves against each other.
Hypatia, who declares her only center to be the sun, is also the only character working in earnest to draw a direct line to the heavens (her experiments with gravity bookend the film). The irony is heavy and ultimately affecting -- a thousand years later Galileo will be jailed for doing similar work. The film's bleak conclusion becomes unbearable in context: Hypatia's death also signals the end of women in positions of intellectual prominence and the beginning of a period known -- not coincidentally -- as the Dark Ages.