Despite its importance as a cathode material in primary alkaline batteries, the structure of γ-MnO2 is still not well determined. Different authors have suggested that a number of different polymorphs, as well as highly disordered phases, may be present in γ-MnO2. The origin of this structural complexity remains largely unexplained. In this paper we use first principles methods to explore the energetics of the MnO2 system. We find a number of low-energy polymorphs with similar energies, suggesting that relatively small changes in the energetics might influence the stable phases. Using nonzero-temperature models we demonstrate that thermal disorder is not the cause of structural disorder in these materials. However, we then show that point (Ruetschi) defects, even in surprisingly low concentrations, have a dramatic effect on the phase stability. We propose that Ruetschi defects may be the key to some of the structural complexity in γ-MnO2, and that any realistic structural study must take them into account.