The chemical reaction of ozone with decanethiol monolayers on Au(111) was characterized using X-ray photoelectron spectroscopy and scanning tunneling microscopy. Our results show that exposure to ozone results in oxidation of the thiol terminus. The reaction initiates at the domain boundary network of the alkanethiol monolayer and propagates into the domains. Above a threshold surface oxygen content, the monolayer converts to a two-dimensional fluid that can subsequently recrystallize to a commensurate monolayer of partially oxidized thiol. Further exposure to ozone results in conversion of the monolayer to a fluid phase and a 10% to 30% expansion of the Au lattice at the Au-thiol interface with concomitant formation of Au islands. Our results demonstrate that crystallographic defects in monolayer films can play an important role in their chemical reactions.