Ion thruster plumes are simulated under a framework that has been recently developed called SUGAR (Scalable Unstructured Gas dynamics with Adaptive mesh Refinement). SUGAR is used to model the momentum exchange (MEX) and charge exchange (CEX) collisions occurring between the neutral and ion species as well as the induced electric field effect due to ions. Multiple AMR meshes are used in order to capture different physical phenomena present in the flow. Streamlines for the flow show that there is a backflow induced due to the combined effect of MEX/CEX collisions and electric field effects. A multiple thruster configuration is also examined to extend the studies to cases where there is no axial or radial symmetry present and therefore can only be modeled with a three dimensional simulation capability. The combined plume structure shows interactions between individual thrusters which the AMR capability captures in an automated manner. Finally, a backflow analysis was done to quantify the conditions present upstream of the thruster.