Pagels argues that one of the most stark differences between orthodox and gnostic Christians was in The Political Impact of Religious Beliefs on Gender and Power. She identifies a correlation between ideas about the gender of the divine and structures of gender and power in human social life. Pagels does not attempt to trace the causality behind this correlation: whether theological ideas inform political structures or vice versa. Instead, she acknowledges the inevitable ambiguity that comes with studying a range of millennia-old cultures, many of which have left little trace of their existence. Similarly, she admits throughout her analysis that the dichotomies she draws between the gnostics and the orthodox are not absolute, remarking, “Gnostics were not unanimous in affirming women—nor were the orthodox unanimous in denigrating them” (66). Her overarching thesis is that theology and politics are inseparable and inform one another in complex and often untraceable ways: 

Our evidence, then, clearly indicates a correlation between religious theory and social practice. Among such gnostic groups as the Valentinians, women were considered equal to men; some were revered as prophets; others acted as teachers, traveling evangelists, healers, priests, perhaps even bishops (60). 

This assertion implies a lament about what might have been. Since The Gnostic Gospels is in part the account of a rivalry between to competing sets of ideas, only one of which would survive and increase in power, Pagels’s description of the gnostic past evokes an alternative future.

Concepts of God are connected in complex ways with the practices of gnostic and orthodox Christians. A key example, for Pagels, lies in each group’s ambivalent relationship to monotheism. For the orthodox, there is the interlocked Trinity of the Father, the Son, and the Holy Spirit, with abstruse theological arguments about the degree to which these three divine beings are both separate and one. Meanwhile, the gnostics had tiered notions of divinity, with sophia, or divine wisdom, at the pinnacle and  the demiurgos, or creator god, occupying a lower plane. Both groups lobbed accusations of polytheism at the other. Just as concepts of divine gender influenced ideas of gender in the human world, Pagels argues that ideas of monotheism were intertwined with how each group handled authority. Specifically, the gnostic rejection of hierarchical authority was reflected in the belief that the creator of the world was a false or lesser deity, with the true deity being a power beyond the creator. “Gnostic modification of monotheism was taken—and perhaps intended—as an attack” (34) upon the hierarchical system of leadership in the orthodox church. In discussing how each group sought to differentiate itself from the other, Pagels emphasizes The Subjective Distinction Between Orthodoxy and Heresy, noting that the contest for power and influence is also a contest for the power to determine what is orthodox and, by extension, what is heretical. 

The difference of hierarchy and egalitarianism is also related to the question of The Primacy of Direct Spiritual Knowledge. As Pagels describes gnosis: “Achieving gnosis involves coming to recognize the true source of divine power—namely, ‘the depth’ of all being. Whoever has come to know that source simultaneously comes to know himself and discovers his spiritual origin: he has come to know his true Father and Mother” (37). Pagels’s key point is that in gnostic theology, anyone, with time and the correct training, can commune with the truly divine. This lends itself to the formation of religious communities that are simultaneously more egalitarian and more elitist than the orthodox church. Unlike gnostic communities, the orthodox church is open to anyone, but to join it is to enter the lower tiers of a rigid hierarchy whose upper tiers—defined by class boundaries contiguous with those of secular life—most can never hope to reach. By contrast, gnostic communities are far less hierarchical, but they are open only to initiates who can convincingly claim to have had a direct experience of the divine. Pagels’s hypothesis is that this combination of social egalitarianism and intellectual or spiritual elitism made gnostic communities permanently small and unstable, while the orthodox church’s rigid power structures and openness to newcomers allowed it to build a cohesive identity and grow into a world-dominating institution.

Pagels suggests that the orthodox view of the creator God resembles earthly authority. “And as God rules over that council in heaven, so the bishop on earth rules over a council of priests” (35). This analogy between heavenly and priestly authority would later extend to a politically useful analogy between God’s authority and that of kings and emperors, creating a symbiotic relationship between church and empire that, though often fractious, would hold for many centuries, further augmenting the political power of the church. Still, Pagels acknowledges that such distinctions are rarely if ever absolute. After all, the orthodox also had a concept of personal conversion experience, like what was experienced by the orthodox writer Justin Martyr (121-122), while gnostics also had teachers and leaders like Valentinian. Despite their differences, the gnostic and orthodox camps drew from similar ideas and had similar needs as groups that required a degree of organization.