The stability of a hypersonic boundary layer for a
$5^{\circ }$ half-angle cone at the Caltech T5 high-enthalpy flow conditions was investigated using direct numerical simulations. For the ‘linear’ stability investigations, the boundary layer was perturbed by small axisymmetric disturbances with very small amplitudes, and for the nonlinear regime, three-dimensional pulse disturbances with larger amplitudes were introduced. The surprising result from these investigations was that the 3D wave packet undergoes strong spatial modulations, which we have not observed for other experimental conditions (e.g. the Purdue BAM6QT). This modulation was found to be directly due to the synchronization between second-mode wave components and vorticity/entropy modes. Furthermore, it was found that a synchronization with slow acoustic waves leads to a sudden and strong emission of acoustic waves deep into the free stream, which was observed for both a linear wave train and a 3D nonlinear wave packet. Therefore, it can be concluded that this is a linear mechanism that is not suppressed by nonlinear effects.