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Future airspace systems are complex in the types of manned and unmanned aircraft and in managing a massive number of these airborne payload containers. Cyber - a highly intangible mix of networking, software, storage, and computing - is vital for superior performance of aircraft and airspace systems. Performance risks, however, emerge from evolving dynamics and unpredictability of an adverse operational environment, both in cyberspace and physical world. This paper proposes a novel cyber-physical system (CPS) framework for aircraft and airspace system design and performance assurance. We present the foundational role of the e-enabled aircraft in the worldwide air transport system modernization. We show how automated air navigation and surveillance depend on tight integration and controlled coordination between in-aircraft systems and off-board systems in ground, air, and space. Based on our seminal concept of “group flight,” we propose a fundamental CPS solution for controlling large volumes of manned and unmanned air traffic using Automatic Dependent Surveillance Broadcast (ADS-B) and Internet Protocol (IP) technology.