The embryological view of biological development is that coordinated gene expression along with cellular physics and migration provides the basis for pattern formation and phenotypic complexity. This stands in contrast to the prevailing view of embodied cognition, which claims that informational feedback between organisms and their environment is key to the emergence of intelligent behaviors, particularly in development. We aim to unite these two perspectives, and call this approach embodied cognitive morphogenesis. Embodied cognitive morphogenesis leads to both fluctuating phenotypic asymmetry and the emergence of information processing subsystems. Our guiding question involves the role morphogenetic symmetry-breaking plays in the differentiation of specialized organismal subsystems, and how this serves as a substrate for the emergence of autonomous behaviors. As the process of embodied cognitive morphogenesis unfolds, we observe three distinct properties: acquisition, generativity, and transformation. A related issue involves the quantitative models we might use to evaluate the increasingly complex structure of embodied cognitive morphogenetic agents. These include tensegrity modeling, differentiation trees, and embodied hypernetworks. These three types of models provide a means to identify the context of various symmetry-breaking events in developmental time. Related concepts that help us define this phenotype further will also be discussed. These include concepts such as modularity, homeostasis, and 4E (embodied, enactive, embedded, and extended) cognition. In conclusion, we will consider these autonomous developmental systems as a process called connectogenesis, or the process of connecting various parts of the emerged phenotype. This approach is useful for the analysis of organisms and the design of bio-inspired computational agents.