The response of the polar ionosphere to magnetospheric storm inputs was modeled. During the ''storm,'' the spatial extent of the auroral oval, the intensity of the precipitating auroral electron energy flux, and the plasma convection pattern were varied with time. The convection pattern changed from a symmetric two-cell pattern with a 20-kV cross-tail potential to an asymmetric two-cell pattern with enchanced plasma flow in the dusk sector and a total cross-tail potential of 90 kV. During the storm there were significant changes in the ion temperature, ion composition, and molecular/atomic ion transition height. The storm time asymmetric convection pattern produced an ion temperature hot spot at the location of the dusk convection cell owing to increased ion-neutral frictional heating. In this hot spot there were significantly enhanced NO+ densitiesand hence molecular atomic ion transition heights. During the storm recovery phase, the decay of the enhanced NO+ densities closely followed the decrease in the plasma convection speed. During the storm, elevated ion temperatures also appeared at high altitudes in the midnight-dawn auroral oval region. These elevated ion temperatures were a consequence of the storm-enhanced topside O+ densities, which provided better thermal coupling to the hot electrons. This region also contained reduced molecular/atomic ion transition heights. These elevated ion temperatures and reduced transition heights persisted for several hours after the storm main phase ended.