A major geomagnetic storm occurred during the second MTEC-E campaign. The storm SC was at 0050 UT on March 31, Dst index reached as low as -358 nT about 8 hours after the SC, and storm recovery phase lasted for about three days. The MU radar (alternate meteor and IS modes), MF radar, OMTI, and GPS-TEC data measured during the campaign (March 23 - April 02, 2001) are used to study the storm- time changes in the upper atmosphere and ionosphere over Japan. The MU radar measured magnetic meridional neutral wind velocity and northward perpendicular plasma drift velocity are incorporated into the Sheffield University plasmasphere ionosphere model (SUPIM) to investigate the relative effects of the storm- time thermospheric neutral wind (direct and indirect effects) and ionospheric electric field on ionospheric height and density, airglow intensity and GPS-TEC.