The flow in the HyShot II scramjet combustor is studied using large eddy simulations (LES). The computations are made feasible by two important modeling ingredients: an equilibrium wall-model and a flamelet-based combustion model. The first objective of the study is to assess the accuracy of this mod-eling approach through a validation study. Comparisons are made between simulation results and those from shock-tunnel experiments at nominal flow conditions, with favorable agreement. The second objective is to study the flow for increased fuel/air equivalence ratios (ERs). A qualitative change in the flow occurs for ER 0.39, with the appearance of a seemingly stable combustor shock-train, similar to standard isolator shock-trains, but occurring spatially co-located with the combustion and heat release. This behavior accurately reproduces that seen in an accompanying experimental study. A detailed flow analysis identifies the factors contributing to the stabilization of the shock-train, and estimates are made of its effect on the overall combustor performance.