This paper presents the formulation, design procedure, and application of a hybrid model predictive control (HMPC) scheme for hybrid systems that is embedded in a mixed logical dynamical (MLD) framework. The proposed approach adopts a three degrees-of-freedom (3DoF) tuning method to accomplish precise setpoint tracking and ensure robustness in the face of disturbances (both measured and unmeasured) and uncertainty. Furthermore, the algorithm employs setpoint and disturbance anticipation to proactively enhance controller performance and potentially reduce control effort. Slack variables in the objective function prevent the mixed-integer quadratic problem from becoming infeasible. The effectiveness of the proposed algorithm is demonstrated through its application in three distinct case studies, which include control of production-inventory systems, time-varying behavioral interventions for physical activity, and management of epidemics/pandemic prevention. These case studies indicate that the HMPC algorithm can effectively manage hybrid dynamics, setpoint tracking and disturbance rejection in diverse and demanding circumstances, while tuned to perform well in the presence of nonlinearity and uncertainty.