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Complex autonomous systems capable of successfully operating independently under ‘known unknowns’ and harsh conditions require paradigm innovation in modern development strategies. In the field of autonomy, developing a system-of-systems which can ostensibly think for itself in the face of ‘unknown unknowns’ is still a field of ongoing research. Maturing the systems architecting and modeling methodologies for developing henceforth named Thinking Autonomous Systems, which are verified with digital mission simulation, can potentially usher in the next generation of artificial intelligence for space exploration. The concept presented in this paper incorporates multiple Model-Based Systems Engineering and simulation methodologies combined as a new paradigm to design a novel, biomimetic thinking autonomy strategy. Anachronistic concepts from classical Kantian philosophy will be leveraged to inspire architectural designs that could be used for complex distributed systems in deep space. To accomplish this, digital transformation of a document-based implementation plan for Thinking Autonomous Systems, generated by experienced NASA software engineers, is implemented for NASA’s Platform for Autonomous Systems by creating descriptive and executable software models in SysML to prototype real-time operating capabilities. This conceptual implementation has been developed by incorporating model-based digital simulations to theorize how a cyberphysical thinking system would achieve specific strategies without crew reliance, while simultaneously being resilient to all operating conditions and remaining functional when devoid of ground communication. Additionally, ensuring that an autonomous system framework is an ethical Artificial Intelligence requires careful consideration of system behavior and accountability, human factors for teaming with a thinking autonomous system, and comparison to other modern approaches used for implementing true autonomy. This paper presents the first steps in formalizing the metacognition required for instantiating a truly Thinking Autonomous System; the approach described symphonizes autonomy characteristics from classical philosophical into a unified software architecture describing human thought. In the future, the foundational models described in this paper can be further leveraged to help advance research into thinking autonomy requirements for future deep space missions as well as for current near-term applications, i.e., living aboard crewed spacecraft like a NASA Gateway cislunar habitat.