: The cyber-physical gap (CPG) is the difference between the 'real' state of the world and the way the system perceives it. This discrepancy often stems from the limitations of sensing and data collection technologies and capabilities, and is an inevitable issue in any cyber-physical system (CPS). Ignoring or misrepresenting such limitations during system modeling, specification, design, and analysis can potentially result in systemic misconceptions, disrupted functionality and performance, system failure, severe damage, and potential detrimental impacts on the system and its environment. We propose CPG-Aware Modeling & Engineering (CPGAME), a conceptual model-based approach for capturing, explaining, and mitigating the CPG, on top of and in sync with the conventional system model, and as an inherent systems engineering activity. This approach enhances the systems engineer’s ability to cope with CPGs, mitigate them by design, and prevent erroneous decisions, actions, and hazardous implications. CPGAME is a generic, conceptual approach, specified and demonstrated with Object Process Methodology (OPM). OPM is a holistic conceptual modeling paradigm for multidisciplinary, complex, dynamic systems, which is also ISO-19450. We analyze the 1979 Three Miles Island 2 nuclear accident as a prime example of the disastrous consequences of unmitigated CPGs in complex systems.