We present a model and observations of the evolution of equatorial ionospheric bubbles during a large auroral electrojet (AE) index increase in the recovery phase of a geomagnetic storm. Using a three-dimensional time-dependent numerical simulation model, we find, for the 19--21 October 1998 storm, that the equatorial bubble evolution is different during storm time as compared to quiet time conditions. We have found that the storm time vertical drift in conjunction with reduced off-equatorial E region shorting is the primary mechanism that distinguishes the large AE increase recovery phase storm time evolution from the quiet time case. Comparison of the simulation model with ground-based storm time radar observations is made.