Contextual interventions pose unique challenges for implementation studies and evaluation research. By contextual, we mean programs that are tightly integrated with the social systems they are seeking to influence or transform. This integration challenges foundational assumptions of intervention science and necessitates the development of innovative approaches to monitoring and evaluation. The W3 (â€˜What Works and Whyâ€™) project piloted the use of complex systems theory and methods (CSTM) to develop program theories for peer and community-led (PCL) programs in HIV and viral hepatitis prevention and health promotion. As a class, these programs have struggled to articulate and theorize their approach to justify their funding and to build an evidence base. CSTM allowed us to articulate detailed program theories based on â€˜mental modelsâ€™ held by program staff and stakeholders. This chapter describes our reflection and adaptation experience as we piloted the CSTM approach inâ”€and asâ”€social research.