Ionospheric disturbances during a magnetic storm on 6 November 2001 were analyzed using total electron content (TEC) calculated from measurements made with a dense GPS receiver network, GEONET, which covers the whole of Japan and F-layer peak parameters obtained by a meridional ionosonde chain which consists of ionosondes at Wakkanai (45.39°N), Kokubunji (35.71°N), Yamagawa (31.20°N), and Okinawa/Ogimi (26.68°N). Maps of TEC as a function of latitude and time were compared with NmF2 and hpF2. A weak to moderate ionospheric positive storm in terms of fOF2 was associated with the magnetic storm. On the other hand, TEC was nearly doubled at all latitudes during the daytime. This event was the effect of a prompt penetrating eastward electric field in the presence of an enhanced equatorward neutral circulation, which was set up prior to the electric field penetration and persisted for more than 24 hours. The ionosphere was raised simultaneously by ∼100 km at the four ionosonde stations. The small ion-neutral collision frequency at high altitudes results in loading of plasma into the plasmasphere. The significant difference in storm signatures between NmF2 and TEC was interpreted as increased upward plasma diffusion, which worked as a sink for the plasma at the F layer peak. The increase in TEC in the plasmasphere, however, was the order of 10 TEC units, which is insufficient to cause the large observed TEC enhancement but was responsible for maintaining the nighttime TEC enhancement. On the bottomside the plasma distribution departed significantly from the photochemical equilibrium due to the upwelling, and the photochemical production tended to adjust it, providing the major source of the great increase in TEC. At night, positive storm conditions both for NmF2 and TEC persisted at latitudes higher than 33°N, which was caused by the downward plasma flux and the equatorward neutral winds. At latitudes lower than 33°N, negative perturbation was observed in the evening hours, caused by the suppression of the evening enhancement of the eastward electric field.