This chapter argues that that Critical Realism, a philosophy of science, when applied in combination with the morphogenetic approach in historical and social research, can contribute to a deeper understanding of social transformation and help to disentangle the structure–agency relations in the maritime disputes in the South China Sea. The ways in which a society (or a group of people) understands maritime space, adopts practices of demarcating borders, and negotiates disputes, cannot be taken as given. Making them subject to historical and social analysis is both scientifically significant and politically relevant, especially with respect to the role of self-reflexivity in social science research into peaceful transformation.