The DoD's ERS initiative calls for affordable, effective, and adaptable systems development. In support of this, a metrics-based analysis framework is introduced to address certain challenges for the design of future C2 military System-of-Systems (SoS). The interpretation of the concept of resilience, as well as a supporting threat analysis procedure for military SoS applications, have been the key driver for the evaluation of a system's ability to maintain its mission capability and health, when under attack due to given threats. An agent-based C2 UAV communication network application has been developed for the demonstration of the framework. Scenario-based case studies that involved communication jamming by the adversary forces are introduced for the evaluation the C2 system's response to a threat, including both degradation and recovery periods.