Collaborative research has become increasingly prominent since the mid-20th century. This article aspires to offer a fundamental ontology of a multidisciplinary research system. As a point of departure, we consider disciplinarity as a restricted language code as noted by Bernstein. The impetus for collaboration is found in a research problem’s transcendence of disciplinary bounds. This article makes several propositions that diverge from the consensus position regarding the formation and dynamics of a multidisciplinary system. Most notably that such a system adheres to the constituent elements of what could be regarded as a complex system, including an ensemble of elements, interactions between these elements, local disorder followed by the emergence of robust order and system memory. We propose that the internal communications and subsequent self-organization of such a system may be conceptualized as orientation signals, or ‘stigmergy’, analogous to those observed in swarms. System robustness, we argue, is a function of the individual researcher’s local autonomy and is, paradoxically, augmented by the weakness of communications across disciplinary bounds, along with the lack of central organization and the emphasis on research novelty. System memory, we argue, manifests itself in the ability of a researcher to change her/his route of inquiry, based on environmental feedback, whereby new information becomes incorporated into the adjusted research methodology. We propose that an emergent intelligence, at the level of the system, expresses itself in the unconcealment of the ‘form’ of the metaproblem. The theoretical model is empirically illustrated using, as an example, the contemporary field of renewable energy research, which is an area primed for collaborative research. It is anticipated that an improved understanding of multidisciplinary research systems provides insights into certain strengths particular to less integrated and self-organized forms of collaborative research along with a framework with which to improve the design and fostering of such systems.