This work investigates the effect of unsteady freestream disturbances on a Mach 6, ramp-induced Shock-Wave/Boundary-Layer Interaction (SWBLI) with discrete roughness elements upstream of the corner. Building on the previous numerical studies investigating the baseflow for the same geometry and flow conditions, the present work analyses the breakdown to turbulence along the ramp of the high-vorticity, “mushroom-like” structure forming in the wake of the roughness as the flow reattaches downstream of the separation bubble. It is found that transition is mainly driven by the amplification of the y-modes promoted by the strong wall-normal gradients present in such high-vorticity structure, especially in the side lobes of the mushroom, where the onset of breakdown is first observed. At the surface, consequence of the transition onset is the localized rise of wall temperature, with a hot streak extending much further along the ramp compared to the steady case.