The upper atmosphere and ionosphere exhibit variability and phenomena that have been associated with planetary and tidal waves originating in the lower atmosphere. To study the effects of these planetary-scale dynamical perturbations on the coupled thermosphere-ionosphere-electrodynamics system a new Whole Atmosphere Model (WAM) is being developed as part of a collaborative project “Integrated Dynamics through Earth's Atmosphere (IDEA)” between National Weather Service's (NWS) Space Weather Prediction and Environmental Modeling Centers, and the University of Colorado. WAM is a 150-layer general circulation model (GCM) based on NWS's operational weather prediction Global Forecast System (GFS) extended from its nominal top altitude of 62 km to over 600 km. IDEA interactively couples WAM with Global Ionosphere-Plasmasphere (GIP) and electrodynamics models. The model extension into a domain of highly variable composition, high temperatures, and very low density requires certain generalization of the standard lower-atmospheric GCM framework. WAM also incorporates all relevant physical processes including those responsible for the generation of tidal and planetary waves in the troposphere and stratosphere. In the absence of artificial boundaries within the model domain these waves freely propagate into the upper atmosphere, growing in amplitude and interacting non-linearly, to eventually dissipate by various physical processes. Long-term simulations reveal realistic seasonal variability of tidal waves with a substantial contribution from non-migrating tidal modes, recently implicated in the observed morphology of the ionosphere. All tides also exhibit a pronounced day-to-day variability, possibly due to modulation by planetary waves. Other phenomena such as the Midnight Temperature Maximum (MTM) at low latitudes, previously associated with tidal effects, are also evident.