Methodologists have urged researchers who use mixed methods to justify their methodological choices and provide greater clarity about the philosophical underpinnings and implications of their approaches. This article outlines the reasoning process undertaken in an endeavor to develop philosophical clarity for an applied, interdisciplinary, mixed methods research project about the communication of scientific evidence in the legal system. I used Greene’s domains of methodology for social inquiry as a framework for addressing reflexive questions about assumptions. Flowing from the domains of values and philosophies, the logic of inquiry was developed before the implications for the integration of findings and reporting of research were outlined. Early engagement in reflexive questioning provided a foundation for methodological refinement throughout the ongoing research journey.