Hypersonic boundary layer research has studied surface features, such as isolated or distributed roughness, extensively for turbulence tripping. However, there are reports of a counterintuitive phenomenon within the literature whereby surface roughness can delay the onset of laminar-turbulent transition. The reports did not attract widespread attention, leaving the phenomenon's underlying mechanism uninvestigated for several decades. A renewed interest in boundary layer control strategies motivated Fong and Zhong in 2012 to conduct an extensive numerical study on what has been termed the ``roughness effect''. The research found that roughness elements immersed within the boundary layer and placed at the synchronization location for a particular unstable frequency can attenuate higher unstable frequencies while amplifying lower unstable frequencies. Thus, providing a passive means to delay laminar-turbulent transition with discrete surface roughness. However, these previous numerical investigations are limited to a flat plate geometry, 2-D spanwise roughness, limited in the scope of their freestream Mach number, and focus exclusively on Mack's second mode instability. In order to advance our knowledge of the roughness effect, the objectives of this dissertation are fourfold: (1) To investigate the roughness effect on a straight blunt cone geometry, (2) To investigate the long-term downstream consequences of the roughness effect, (3) Provide experimental evidence of second mode attenuation in a flow with a growing boundary layer containing a range of unstable frequencies, and the consequences of off-design flow conditions, and (4) To investigate the appearance of the supersonic mode in a low-enthalpy warm wall flow of the current study. A combined approach of direct numerical simulation, body-fitted surface roughness, and linear stability theory are used to numerically investigate the roughness effect. Four cases are computed as part of the research objective. Case C.1 is a Mach 8 flow computed for the design of a passive transition-delaying roughness configuration, along with studying the roughness effect on a straight blunt cone. Case C.1-Ext is a longer cone simulation of C.1 and is computed to investigate the long-term downstream response of the roughness effect. C.2 is similar to C.1 except for a smaller nose radius and is computed for experimental validation. The last case, C.3, is a Mach 5 flow and is computed to study the roughness effect on a straight blunt cone in off-design flow conditions and for experimental validation. The first objective to investigate the roughness effect on a straight blunt cone advances the research from a flat plate to more realistic test article geometries. Much of the experimental work done in hypersonic boundary layer stability research is done on straight cones due to the axisymmetric flows in hypersonic wind tunnels. The investigation found that the roughness effect behaves like a flat plate where unstable frequencies higher than the synchronization frequency are attenuated, and lower frequencies are amplified. The investigation also found that some flow features around the roughness elements, such as separation zones, are either smaller in size or absent in conical flow fields. The investigation also confirmed that the second mode's attenuation is a result of the element's proximity to the synchronization location and not due to its proximity with the branch I/II neutral points. The long-term downstream effect of second mode attenuation is also investigated for a single roughness and roughness array. The numerical investigation found that the range of targeted frequencies is attenuated as expected, especially for the roughness array, which proves to be effective at attenuating unstable frequencies over a longer distance. However, the amplitudes of frequencies below the targeted range grow many times higher than they would have otherwise on a cone with no roughness. The passive transition-delaying control strategy, rather than dissipating the disturbance energy, acts to transfer the energy to lower unstable frequencies, guaranteeing eventual turbulent transition. The result demonstrates that roughness must be applied to the entire cone to have an effective control strategy. The experimental results in this dissertation come from a joint numerical and experimental investigation of transition-delaying roughness with Dr. Katya Casper at Sandia National Laboratories. A numerical simulation is undertaken to design a surface roughness array that would attenuate Mack's second mode instability and maintain laminar flow over a Mach 8 hypersonic blunt cone. Multiple experimental runs at the Mach 8 condition with different Reynolds numbers are performed, as well as an off-design Mach 5 condition. The roughness array successfully delays transition in the Mach 8 case as intended but does not delay transition in the Mach 5 case. For validation and further analysis, numerical cases C.2 and C.3 are computed using the Mach 8 and Mach 5 experimental flow conditions. Stability analysis of case C.2 shows that the roughness array is adequately designed to attenuate the second mode. Analysis of case C.3 reveals the Mach 5 boundary layer is dominated by Mack's first mode instability and is not attenuated by the array. This investigation of multiple flow conditions combined with experimental results helps validate the numerical code and provides empirical evidence for the roughness effect. While investigating transition delaying surface roughness, acoustic-like waves are observed emanating from the boundary layer of case C.1-Ext. The acoustic-like wave emissions are qualitatively similar to those attributed to the supersonic mode. However, the supersonic mode responsible for such emissions is often found in high-enthalpy flows with highly cooled walls, making its appearance in a flow with relatively low freestream enthalpy and a warm wall unexpected. Stability analysis on the steady-state solution reveals an unstable mode S with a subsonic phase velocity and a stable mode F whose mode F- branch takes on a supersonic phase velocity. The stable supersonic mode F is thought to be responsible for the acoustic-like wave emissions. Unsteady simulations are carried out using blowing-suction actuators at two different surface locations. Analysis of the temporal data and spectral data reveals constructive/destructive interference occurring between a primary and a satellite wave packet in the vicinity of the acoustic-like wave emissions, which has a damping effect on individual frequency growth. Based on this study's results, it is concluded that a supersonic discrete mode is not limited to high-enthalpy, cold wall flows and that it does appear in low-enthalpy, warm wall flows; however, the mode is stable.