Composition and photochemistry in the atmospheric region between 45 km and 120 km is studied by microwave spectroscopy measurements and by photochemical and dynamical modeling of the region. The trace chemical species are measured at the Kitt Peak AZ microwave facility, and include NO, HCN, N2O, CO, and O3 (0,0,0), (1,0,0), (0,1,0), (0,0,1), along with the major species O2. New measurements are combined with data gathered since 1992 to investigate middle-atmosphere response to solar flux and magnetic storm forcing, as well as the relative importance of planetary wave transport in the context of seasonal transport mechanisms. The fact that current photochemical models can be adjusted to fit O3, OH, and HO2 data in the upper stratosphere, or to do so in the mesosphere, but not self-consistently in both regions, is reconciled by this new effort using realistic transport parameterizations in each region. The first simultaneous measurements of ozone in the ground and three distinct vibrational states quantifies the non-local thermodynamic equilibrium in those states, permitting improved interpretation of satellite infrared measurements of ozone. The response of trace species in this atmospheric region is expected to provide a very sensitive monitor of secular chemical change, be those driven by either natural or anthropogenic forces.