This study presents the Global Self-Consistent Model of the Thermosphere, Ionosphere and Protonosphere (GSM TIP) numerical simulations of the 9–14 September 2005 geomagnetic storm effects in the middle- and low-latitude ionosphere. Recent modifications to the GSM TIP model include adding an empirical model of high-energy electron precipitation and introducing a high-resolution (1 min) calculation of region 2 field-aligned currents and a cross-cap potential difference. These modifications resulted in better representation of such effects as penetration of the magnetospheric convection electric field to lower latitudes and the overshielding. The model also includes simulation of solar flare effects. Comparison of model results with observational data at Millstone Hill (42.6°N, 71.5°W, USA), Arecibo (18.3°N, 66.8°W, Puerto Rico), Jicamarca (11.9°S, 76.9°W, Peru), Palmas (10.2°S, 48.2°W, Brazil), and San Jose Campos (23.2°S, 45.9°W, Brazil) shows good agreement of ionospheric disturbances caused by this storm sequence. In this paper we consider in detail the formation mechanism of the additional layers in an equatorial ionosphere during geomagnetic storms. During geomagnetic storms, the nonuniform in height zonal electric field is generated at the geomagnetic equator. This electric field forms the additional layers in the F region of equatorial ionosphere.