Three dimensional turbulent simulations with combustion modeling are employed to understand fundamental phenomena encountered in the HIFiRE-2 scramjet flowpath. Experimental data from the ground test campaign as well as a grid resolution study is used to validate the results of the simulations. These confirmed results are then leveraged to explain the physics of dual and scramjet-mode operation in a steady sense, including detailed examinations of shock structure, boundary layer separation, and combustion chemistry. Initial results of unsteady simulations are used to investigate the process of mode-transition, and a simplified heat release model is developed and tested. Simulations of the flight test are presented and contrasted with the ground test results to characterize the effects of the inlet on the boundary layer development and internal shock structures. Overall, agreement with ground test results is excellent, and the simulations show highly complex three dimensional structures to be present in the flow. Boundary layer separation induced shock / boundary layer interactions dominate dual-mode operation, while at higher Mach numbers a flameholding effect of the barrel shock from fuel injection is striking. The effects of the inlet are found to be of great importance to accurately model flight tests, however, the same macro-scale effects as observed in the ground test simulations are dominant.