There is great interest in understanding how the thermosphere-ionosphere system responds to geomagnetic storms. New insights are possible using the new generation of fully coupled three-dimensional models, together with extensive ionospheric databases. The period of postsolar maximum geomagnetic storms in October and November 2003 were some of the largest storms ever recorded. In this paper, we explore how the thermosphere-ionosphere system responded to the onset of the 20 November 2003 geomagnetic storm, using the NCAR TIMEGCM. The model simulates dramatic changes in the thermospheric equatorward winds, O/N2, and corresponding ionospheric electron densities. The model is used as a framework to interpret an increase in the observed ionospheric total electron content, and F region electron density, in the European and North African sector, in terms of changes in the neutral gas. Corresponding compositional effects observed by the GUVI instrument on the TIMED satellite lend credence to the model results. We describe some of the important physical processes that will affect planning for the utilization of measurements from the Geospace investigations in NASA's Living With a Star Program. The study illustrates the value of measuring both the neutral and ionized gases, of obtaining quasi-global views from imaging instruments, and the synergy between satellite data, ground-based measurements, and models.