A theory of equatorial thermosphere-ionosphere-plasmasphere (magnetosphere) disturbances creating field aligned irregularities is extended here. Further development is given of the hypothesis of the transfer of electrostatic fields and currents from the B-region dynamo to the conjugate F-region, topside ionosphere, and plasmasphere, involving field-aligned currents. Conditions are found such that dynamo action in the ionosphere controls the formation of large-scale magnetic field-aligned irregularities. Sporadic-E layers involving Fe+, and/or other long-lasting ions, may play a special role in the process. General conditions are found under which the discharge of ionospheric currents across the geomagnetic field in the magnetosphere is a significant factor. An energy analysis is conducted of the processes involved in the formation of the irregularities. This suggests that there is a large class of equatorial ionosphere-plasmasphere irregularities whose source of energy is in the conjugate -regions. Alternatively stated, winds and gravity waves in the conjugate point B-regions are a significant source of energy for the equatorial F-region and topside plasmasphere where it is dissipated as joule heat, viscous heating and compressional heating of plasma followed by heat conduction in the neutral gas. Dynamo processes in the conjugate B-regions are a significant source of energy also for the nightside equatorial thermosphere at F region and higher altitudes.