The focus of this paper is to present a game theoretical modeling and simulation framework for the integration of Unmanned Aircraft Systems (UAS) into the National Airspace system (NAS). The problem of predicting the outcome of complex scenarios, where UAS and manned air vehicles co-exist, is the research problem of this work. The fundamental gap in the literature in terms of developing models for UAS integration into NAS is that the models of interaction between manned and unmanned vehicles are insufficient. These models are insufficient because a) they assume that human behavior is known a priori and b) they disregard human reaction and decision making process. The contribution of this paper is proposing a realistic modeling and simulation framework that will fill this gap in the literature. The foundations of the proposed modeling method is formed by game theory, which analyzes strategic decision making between intelligent agents, bounded rationality concept, which is based on the fact that humans cannot always make perfect decisions, and reinforcement learning, which is shown to be effective in human behavior in psychology literature. These concepts are used to develop a simulator which can be used to obtain the outcomes of scenarios consisting of UAS, manned vehicles, automation and their interactions. An analysis of the UAS integration is done with a specifically designed scenario for this paper. In the scenario, a UAS equipped with sense and avoid algorithm, moves along a predefined trajectory in a crowded airspace. Then the effect of various system parameters on the safety and performance of the overall system is investigated.