Using the sounding measurements from the radio plasma imager on IMAGE and a plasma density inversion algorithm, we derive the plasma density profiles along the magnetic field in a few L shells every 14 hours at magnetic local noon before, during, and after the 31 March 2001 magnetic storm. An empirical model of the plasmaspheric plasma density distribution is derived as a reference using the measurements before the storm. During the storm the equatorial plasma was substantially depleted in a range of L shells. The flux tubes were refilled after the storm. The filling ratio, the equatorial plasma density normalized by its quiet time value before the storm, is introduced to assess the time evolution of the depletion and refilling processes. The depletion, more than two thirds of the quiet time content, appeared to occur rather quickly after the storm onset, as determined by the limited temporal resolution of the measurements. The refilling proceeded, although more slowly than the depletion process, significantly faster than the theoretical prediction of a 3-day timescale. Dynamic structures are observed in situ and confirmed by the extreme ultraviolet imager (EUV) measurements.