The generation mechanisms and physical characteristics of mountain and inertia-gravity waves in high impact UTLS environments are investigated for real atmospheric conditions. The three-dimensional character of the generated waves is confirmed with analysis of co-spectra of the vertical and horizontal velocities. The polarization relation between the horizontal wind components is evidenced by the hodograph of the horizontal wind vector, further confirming the upward energy propagation. Three-dimensional instabilities in non-parallel shear stratified flows such as those induced by mountain and polarized inertia-gravity waves in stably stratified stratospheric environments are characterized by the polarized Richardson number. To resolve multi-scale physical processes of wave breaking and laminated structures in the UTLS region, vertical nesting and adaptive vertical gridding have been developed and applied in the nested, high resolution, coupled mesoscale/microscale simulations. The fully three-dimensional, moist, compressible Navier-Stokes Equations are solved with a stretched, adaptive grid in the vertical and improved resolution in the UTLS region. For nesting, both lateral and vertical boundary conditions are treated via relaxation zones where the velocity and temperature fields are relaxed to those obtained from the mesoscale inner nest. Real-case simulations based on initial and boundary conditions from high resolution T799L91 ECMWF analysis data are conducted for the Terrain-induced Rotor Experiment (T-REX) campaign of measurements. Localized sharp shear layers and stiff gradients of potential temperature and vertical velocity are predicted above the tropopause and in the lower stratosphere within the embedded microscale nest. We describe fully three-dimensional multi-scale dynamics of laminated structures and non-equilibrium processes observed in the UTLS region during TREX. Depending on atmospheric conditions, the gravity waves might be trapped at the altitude of the atmospheric disturbance, break or propagate into higher altitudes acquiring characteristics of inertia-gravity waves.