The effects of geomagnetic activity on the middle-latitude ionosphere and thermosphere which were monitored by the Millstone Hill incoherent scatter radar during a series of large magnetic substorms during February 7--10, 1986, are presented and discussed. These data are compared with similar measurements from the geomagnetically undisturbed January 1986 period described in paper 1 (Hagan and Salah, this issue). The effects of ion-neutral frictional heating associated with magnetic substorms are initially quantified by comparative analyses of the ion temperatures from the January and February 1986 experiments. Ion temperature enhancements of 900¿--1500¿ K were observed between 30¿ and 50¿ N during the most intense substorm. Thermospheric temperature and wind determinations from the two periods are similarly compared. Exospheric temperature enhancements of 200¿--500¿ K characterize the entire storm period, with larger enhancements during the most disturbed times. Thermospheric temperatures remained elevated well into the recovery period. The accuracy of the Joule heating correction to the temperature determinations for the February experiment is measured against three cases; no neutral motion, neutral motion equal in magnitude and direction to the ion flow, and neutral motion equal in magnitude but opposite in direction to the ion flow. Finally, thermospheric meridional wind fields are presented and discussed. Southward surges of 400--600 m/s occurred near 2400 UT on February 7 and 8. Additionally, residual southward winds of 200--500 m/s were strong enough to reverse the northward flow, driven by the diurnal pressure gradients which characterize magnetically undisturbed conditions, during the afternoon of February 8. The thermospheric meridional wind field recovered rapidly as soon as the geomagnetic activity subsides. ¿ American Geophysical Union 1988