The film frequently foregrounds Hypatia’s status as a female intellectual in a male-dominated culture, which feels emphasized for modern sensibilities. Her character is depicted with an almost flawless rationality and virtue, overshadowing the development of other characters. Historical nuance sometimes takes a backseat to highlighting her victimhood and progressive ideals.

Agora extensively critiques early Christianity, portraying religious faith mainly as an instrument of oppression and anti-intellectualism. Family and tradition are often depicted as regressive, with Hypatia positioned as the enlightened exception. This approach undermines historical religious and cultural contexts in favor of modern skepticism.

Traditional or religious perspectives are almost exclusively negative, with dissenters shown as zealots or antagonists. The film offers little room for sympathetic or nuanced views from the non-secular camp, exemplifying a one-sided presentation that aligns closely with contemporary ideological consensus.