During magnetic storms the development of equatorial plasma bubbles (EPBs) and distributions of thermospheric densities are strongly influenced by the histories of imposed magnetospheric electric (ε<sub>M</sub>) fields. Periods of intense EPB activity driven by penetration ε<sub>M</sub> fields in the main phase are followed by their worldwide absence during recovery. A new method is applied to estimate global thermospheric energy (<I>E</I><sub>th</sub>) budgets from orbit-averaged densities measured by accelerometers on polar-orbiting satellites. During the main phase of storms <I>E</I><sub>th</sub> increases as long as the stormtime ε<sub>M</sub> operates, then exponentially decays toward quiet-time values during early recovery. Some fraction of the energy deposited at high magnetic latitudes during the main phase propagates into the subauroral ionosphere-thermosphere where it affects chemical and azimuthal-wind dynamics well into recovery. We suggest a scenario wherein fossils of main phase activity inhibit full restoration of quiet-time dayside dynamos and pre-reversal enhancements of upward plasma drifts near dusk denying bottomside irregularities sufficient time to grow into EPBs.