This chapter presents the interconnection between modeling, simulation, and uncertainty used for understanding and analyzing complex systems such as virtual reality. The integration of modeling, simulation, and uncertainty is essential for robust decision-making that represents the crucial feature of a complex system. By accounting for uncertainties during the modeling phase, one can create more resilient systems and develop strategies that are effective under a range of possible future scenarios. Sensitivity analysis, uncertainty quantification, and scenario-based simulations are common practices employed to better understand how uncertainties affect outcomes. Modeling and simulation serve as tools for exploring and analyzing complex systems, while effectively addressing uncertainty is crucial for making informed decisions based on these analyses.