Repeated phase transformations in materials are accompanied by a decay of material properties. For example, the repeated cycling of multiferroic materials through phase transformation causes its Curie temperature to migrate. Similarly, in intercalation materials, repeated charge/discharge processes are accompanied by structural damage and hysteresis. The origins of fatigue and hysteresis in phase transformation materials is not well understood. Our research aims to investigate the delicate interplay between atomic scale crystallographic changes and the continuum scale microstructural evolution that shapes physical properties of phase transformation materials. We focus on one candidate material—intercalation materials that are used as electrodes in rechargeable batteries—and are developing continuum models to gain quantitative insights into how crystallographic microstructures nucleate and grow during phase transformation.