Hybrid rocket propulsion is deemed to be advantageous to its solid and liquid counterparts for the safety nature of the designs. With the proposed innovation in this research using dual-vortical-flow (DVF) chambers, hybrid rocket engines can also deliver thrust performance close to that of kerosene liquid engines but with much reduced production cost. Based on this new approach and cost saving strategy, a multifunction sounding rocket system is designed with the features of high performance hybrid combustion, trajectory following flight controls, enhanced science experiments, and an advanced payload recovery method. High fidelity numerical modeling design approach and hot-fire experiments are employed to assess the overall performance of the DVF hybrid rocket engines that has roll control capability embedded in the design. Three basic flight trajectory designs are proposed in this study, namely the traditional standard parabolic trajectory, a TASE (Trajectory Augmented Science Experiments) maneuver and a HOOK (Homing Oriented Operation Kernel) maneuver. The TASE maneuver is designed for maximizing the measurement capabilities of the instruments for atmospheric and ionosphere data profiles. The HOOK maneuver is aiming at improving the success in science payload recovery and in reducing the search and recovery efforts. To achieve these goals, a high performance and reliable flight control system is critical, that incorporates the throttling capability of the DVF hybrid rocket engine, which is one of the key development aspects of this study.