While lithium ion batteries with electrodes based on intercalation compounds have dominated the portable energy storage market for decades, the energy density of these materials is fundamentally limited. Today, rapidly growing demand for this type of energy storage is driving research into materials that utilize alternative reaction mechanisms to enable higher energy densities. Transition metal compounds are one such class of materials, with storage enabled by "conversion" reactions, where the material is converted to new compound upon lithiation. MoS2 is one example of this type of material that has generated a large amount of interest recently due to its high theoretical lithium storage capacity compared to graphite. Here, cryogenic scanning transmission electron microscopy techniques are used to reveal the atomic-scale processes that occur during reaction of a model monolayer MoS2 system by enabling the unaltered atomic structure to be determined at various levels of lithiation. It is revealed that monolayer MoS2 can undergo a conversion reaction even with no substrate, and that the resulting particles are smaller than those that form in bulk MoS2, likely due to the more limited 2D diffusion. Additionally, while bilayer MoS2 undergoes intercalation with a corresponding phase transition before conversion, monolayer MoS2 does not.