The increasing use of unmanned aircraft (UA) in military operations will give rise to the variety of missions and the UA performing them. To effectively predict and evaluate these complex UA operations, this paper introduces a multi-mission model for heterogeneous agent simulations. Missions typically performed by UA agents were reviewed and selected for modeling. The most important missions were assigned key performance parameters and modeled based on said parameters. The individual components of the model and their functions are described, and the developed model was applied to study the effect of including multiple agents or heterogeneous agents in a system. Additionally, a number of different UA operational strategies were studied and the performance of each model was analyzed depending on agent composition and operational strategy.