Propagating convective storms across the US northern plains are often coupled with preexisting midtropospheric perturbations (MPs) initiated over the Rocky Mountains. A companion study (Part I) notes that such MPs occur most commonly at 12 UTC (early morning) and 00 UTC (late afternoon). Using a regional reanalysis and a general circulation model (GCM), this study investigates how such a bimodal distribution of the MP frequency is formed. The results point to two possible mechanisms working together while each has a different timing in terms of maximum effect. The diurnal evolutions between the midtropospheric flows over the Rockies and over the Great Plains are nearly out-of-phase due to inertial oscillation. During the nighttime, the westerly flows at 700–500 mb over the Rockies intensify while flows at the same level over the Great Plains turn easterly. These two flows converge over the eastern Rockies and induce cyclonic vorticity through vortex stretching. After sunrise, the convergence dissipates and the cyclonic vorticity is redistributed by horizontal vorticity advection, moving it downstream. This process creates a climatological zonally propagating vorticity signal which, in turn, facilitates the early-morning MP genesis at 12 UTC. The analysis also reveals marked dynamic instability conducive to subsynoptic-scale disturbances in the midtroposphere over the Rockies. Strong meridional temperature gradients appear over the north-facing slopes of the Rockies due to terrain heating to the south and the presence of cooler air to the north. This feature, along with persistent vertical shear, creates a Charney–Stern type of instability (i.e. sign changes of the meridional potential vorticity gradient). Meanwhile, the development of terrain boundary layer reduces the Rossby deformation radius which, subsequently, enhances the likelihood for baroclinic short waves. Such effects are most pronounced in the late afternoon and therefore are supportive to the MP genesis around 00 UTC. Examination of GCM experiments with and without orography further supports the critical role of the Rocky Mountains and its associated boundary layer impacts on the formation of MPs.