A computational strategy based on coupling density functional theory, variational transition state theory, and a microscale materials morphology description unravels details of the defect-induced effect on the surface decomposition of molecular crystals. The technique allows us to resolve the earliest stages of decomposing solids, even for very complex materials and for ultrafast chemical reactions. A comparative analysis of chemical decomposition reactions in HMX with progressively increasing system complexity (an isolated HMX molecule; a perfect single HMX crystal; a defect-containing, porous, and granular HMX crystal) demonstrates that the initiation of the material's degradation can be effectively manipulated by changing the crystal morphology. The activation barriers, reaction constants, and corresponding reaction rates are obtained as a function of molecular environment (a molecule in a vacuum in an ideal bulk crystal, on a surface or interface, and on a defect in a solid), and decomposition times are predicted. The computational approach can be applied to any other material and system.