Preliminary design of low-thrust interplanetary missions is a highly complex process. The mission designer must choose discrete parameters such as the number of flybys, the bodies at which those flybys are performed, and in some cases the final destination. In addition, a time-history of control variables must be chosen that defines the trajectory. There are often many thousands, if not millions, of possible trajectories to be evaluated, which can be a very expensive process in terms of the number of human analyst hours required. An automated approach is therefore very desirable. This work presents such an approach by posing the mission design problem as a hybrid optimal control problem. The method is demonstrated on hypothetical missions to Mercury, the main asteroid belt, and Pluto.