Highly-resolved Direct Numerical Simulations (DNS) were carried out to investigate the dominant nonlinear mechanisms of three-dimensional wave packets in a hypersonic boundary layer. The wave packets were generated with a short-duration pulse in a flared cone boundary layer at Mach 6 and zero angle of attack. For these simulations the same cone geometry and the same flow conditions as in the flared cone experiments conducted in the Boeing/AFOSR Mach 6 Quiet Tunnel (BAM6QT) at Purdue University were employed. The computational domain covered a large extent of the cone in the azimuthal direction to allow for a wide range of azimuthal wavenumbers (kc ) and to include shallow instability waves with small azimuthal wavenumbers. Two different simulations were carried out for which the wave packets were initialized with a pulse forcing amplitude of 0.01% and 0.1% of the free-stream velocity. The disturbance spectra for both forcing amplitudes provided conclusive evidence that the so-called fundamental resonance was the dominant nonlinear mechanism. Furthermore, contours of the time-averaged Stanton number exhibited “hot” streaks on the surface of the cone within the wave packet. Hot streaks have also been observed in the Purdue flared cone experiments using temperature sensitive paint (TSP) and in numerical investigations using DNS. The spanwise streak spacing obtained from the wave packet simulations agrees well with that observed in the Purdue quiet tunnel experiments.