This talk outlines an effort to understand the impact of inlet isolator physics on the combustion of scramjet engines under actual flight relevant high speed conditions. The objective of the proposed work is to gain a fundamental understanding of the feedback mechanism between the boundary layer structures and separated flow in the isolator and the corresponding combustion dynamics that can lead to instabilities and/or unstart. An experimental effort is presented where unstart and combustion instabilities are investigated in an optically accessible axisymmetric scramjet model in a free flow high enthalpy flow tunnel (ACT-II). The effort is coupled with advanced spatially resolved diagnostics of both the isolator and the combustor region to obtain critical insight into the key physics, and to provide foundational data for numerical simulation efforts.