Field-aligned currents play an important role in magnetosphere-Ionosphere (M-I) coupling. These currents can act as the source of free energy for a number of kinetic instabilities which lead to plasma energization. The instabilities may also lead to the formation of plasma density cavities or enhancements, and these in turn play a role in the escape of heavy ions from the ionosphere. All of these factors affect plasma transport properties in the M-I system, and the high latitude ionospheric plasma must also respond to both magnetospheric and corotational electric fields. This study will examine the role of kinetic instabilities to M-I coupling and plasma transport processes. A multi-scale model will be used to generate simulations which can be incorporated in other global models, such as those used in space weather research and forecasting.