Despite the numerous advances in control theory over the past decades, humans’ versatility in controlling complex systems is still irreplaceable due to their adaptive capabilities. Yet, when it comes to implementing adaptive controllers in piloted applications, unfavorable interactions of human pilots with control systems are observed in certain applications. While several studies exist in the literature that investigate pilot-controller interactions, they are primarily based on linear and fixed dynamics. These studies are useful to study the ideal system behavior, however, they may not be helpful in analyzing uncertainties and failures in system dynamics and the adaptive response of the human operator to these undesired occurrences. In this paper, we fill this gap by proposing a closed-loop system analysis consisting of adaptive dynamics for both the pilot and the flight control system. This analysis can offer guidance in designing adaptive control architectures to enhance safety measures in real-world manned applications.