The UAS autonomy architecture proposed in this paper is a new approach in the field of trustworthiness of UAS and insertion into civil airspace. In contrast to common research on UAS insertion, the focus is on providing functional redundancy in flight guidance and mission management, which is important in case of data link loss especially. The system design described in this article envisages the introduction of an on board assistant system implemented as an on board software agent, which is based on cognitive automation. The Cognitive System Architecture COSA2 is used to implement the agent realizing the cooperative control paradigm aboard a UAV for the first time. Besides the description of domain knowledge modeling for the implementation of the agent, a procedural method to enable co-operative human agent interaction with respect to basic behavioral requirements on assistant systems is presented. Finally, a simulation environment is used for evaluating both the cognitive agent’s performance as well as the overall system performance enhancement.