Direct Numerical Simulations (DNS) were carried out in order to investigate the laminar-turbulent transition process of a hypersonic boundary-layer on a flat plate. The conditions of the Boeing/AFOSR Mach 6 Quiet Tunnel (BAM6QT) at Purdue University were used for the simulations. Results from a three-dimensional nonlinear wave packet simulation indicated that all of the “classical” nonlinear mechanisms (fundamental resonance, subharmonic resonance, oblique breakdown) are possible breakdown scenarios for a hypersonic boundary-layer on a flat plate. A detailed investigation of the secondary instability regime showed that the fundamental resonance was much stronger than the subharmonic resonance. High-fidelity “controlled” breakdown simulations for first mode oblique and second mode fundamental, exhibited the development of “hot” streak patterns on the surface of the flat plate. Streamwise “hot” streaks were also observed in the flared cone experiments at the BAM6QT facility and in DNS of high-speed transition for straight and flared cones. For the flat plate the fundamental resonance and the oblique breakdown mechanisms lead to a breakdown to turbulence. The transition region of the second mode fundamental breakdown is longer than for the first mode oblique breakdown.