A key scientific challenge during the outbreak of novel infectious diseases is to predict how the course of the epidemic changes under different countermeasures that limit interaction in the population. Most epidemiological models do not consider the role of mutations and heterogeneity in the type of contact events. However, pathogens have the capacity to mutate in response to changing environments, especially caused by the increase in population immunity to existing strains and the emergence of new pathogen strains poses a continued threat to public health. Further, in light of differing transmission risks in different congregate settings (e.g., schools and offices), different mitigation strategies may need to be adopted to control the spread of infection. We analyze a multi-layer multi-strain model by simultaneously accounting for i) pathways for mutations in the pathogen leading to the emergence of new pathogen strains, and ii) differing transmission risks in different congregate settings, modeled as network-layers. Assuming complete cross-immunity among strains, namely, recovery from any infection prevents infection with any other (an assumption that will need to be relaxed to deal with COVID-19 or influenza), we derive the key epidemiological parameters for the proposed multi-layer multi-strain framework. We demonstrate that reductions to existing network-based models that discount heterogeneity in either the strain or the network layers can lead to incorrect predictions for the course of the outbreak. In addition, our results highlight that the impact of imposing/lifting mitigation measures concerning different contact network layers (e.g., school closures or work-from-home policies) should be evaluated in connection with their effect on the likelihood of the emergence of new pathogen strains.