This chapter examines the trajectory of a research project on militant organizations’ adaptation that began as a “classic” case comparison and was “re-cased” into an explicitly network-based comparison of intra-organizational networks. In doing so, it outlines a method of comparison focused primarily on roles, relations, and emergence rather than on organizational form or behavior. The chapter starts by discussing the project’s initial research design, which proposed a study of militant organizations across three Palestinian refugee camps in Lebanon that largely adhered to Millian logic. The project dedicated extensive research time to establishing a pre-invasion “control” by seeking to demonstrate pre-shock organizational uniformity across the communities under study. However, the evidence gathered often complicated or contradicted logics of control, independence, causality, and identification that undergird dominant approaches to comparison. Rather, it repeatedly indicated that complex, relational, often contingent interactions among geographic environment, communities’ interpretations of violence, and organizational structures influenced outcomes of interest. The chapter leverages this experience to establish core tenets of a broader approach to studying organizational change in comparative perspective.