The interaction between a hypersonic flow at M=6 over a flat plate, a wedge and a cone with a side jet is investigated using the direct simulation Monte Carlo (DSMC) method. The presence of the jet creates a complex flowfield near the surface as multiple circulation regions, separation, reattachment and bow shocks are observed. Nevertheless the interactions between these multi-scale structures are captured with the DSMC method. The unsteadiness resulting from the shock-shock, shock-boundary layer and shock-shear layer interactions are observed and some initial characterization is provided. Preliminary data from experiments performed at a quiet wind tunnel for a cone geometry are presented.