Caring and rehabilitation of spinal cord injuries have greatly evolved. But standard training still heavily relies on manual mobilization. Which results in short training periods, but also prevents the patient's muscles from contracting, if voluntary control is lost. In order to cope with these issues the Fondation Suisse pour les Cyberthèses (FSC) in collaboration with the Laboratoire de Systèmes Robotiques (LSRO) from EPFL initiated the Cyberthosis project. The main idea is the combination of motorized orthoses and closed loop muscle stimulation in order to enable an active participation of the patient. This work focuses on the control of the WalkTrainer, both of the motors and the muscle stimulation. First optimal trajectory generation is discussed. Second, a novel off line EMG based muscle model and closed loop stimulation algorithms will be presented. Third, a new rehabilitation strategy, combination of the two previous findings, will be introduced. That strategy was successfully tested on 6 paraplegic subjects.