The chapter revisits the System of System Methodologies (SoSM) and suggests that use of the SoSM as a framework for defining methodological assumptions is difficult when the concerned methodologies have significantly different meanings for one axis of the framework—“system” complexity. It is suggested that the purpose of the underlying system can provide a more appropriate frame for defining system approaches—such purpose being defined as interaction or transformation (Mathiassen & Nielsen, 2000). The chapter also uses aspects of critical realism to provide insights into the SoSM and the critical theory underpinning the framework. The SoSM helped to highlight the neglect of coercive situations and ultimately helped prompt the development of critical systems theory which is focused on three basic commitments, critical awareness, methodological pluralism, and emancipation. Maru and Woodford (2001) recently argue that the focus on emancipation has been relegated due to a concentration on pluralism. This chapter suggests that this is a logical outcome of the epistemological focus of the underlying critical theory of Habermas. The Habermas focus on the epistemological or knowledge-based aspects of the development process must necessarily relegate the importance of ontological matters such as the conditions necessary for emancipatory practice. This chapter proposes that the philosophy of critical realism has insights to offer through its highlighting of the ontological issues in more detail and in arguing for a recognition of the deep structures and mechanisms involved in social situations.