The present paper explains how an 18 year-old boy, who suffered an incomplete spinal cord injury (SCI) at the Cervical 5/6 levels, could achieve a near-complete recovery within 3 years of coordination dynamics therapy (CDT). The anatomically incomplete SCI was evident on MRI (Magnetic Resonance Imaging) which showed that 50% of the cord tissue was destroyed at the injury site. The administered CDT included the training of crawling, walking, running, jumping, and exercising on special CDT devices. Now 21 years old, this chronically injured young man cannot only walk independently, but he can also run and jump. He has attained full bladder control and is off all medications. The underlying mechanism contributing to this excellent recovery will have to be explained in the framework of the System Theory of Pattern Formation. In this framework the clinical improvement can be quantified in terms of coordination dynamics values, behavioural description of movement performance, analysis of motor patterns, and surface electromyography (sEMG) recorded during the movements. The impaired ability of the injured nervous system to self-organize is evidenced by deteriorated motor programs recorded with sEMG, unstable movement performances, and asymmetric attractor layouts in coordination dynamics recordings. On the other hand, the improvement of motor programs after CDT could also be measured by surface EMG, including measurements of antagonistic action of muscles and also by the improvement of the mean stability of motor patterns. These indicators of improving motor programs could be correlated with clinical improvement in certain motor performances like running and jumping. The recovery could mainly be achieved through a functional reorganisation as was indicated by the absence of significant improvement in the power of the quadriceps femoris muscles. The performances of turning on the special CDT device against high loads were diagnostic for the extent of repair of the integrative functions of the CNS. The cure of urinary bladder function is probably attributable to learning transfer from stereotyped, coordinated, integrative movements to the neural networks involved in bladder control. Since the patient received sub-optimal CDT, it took more than 3 years for the recovery. It appears that the repair of the integrative functions of the CNS need longer periods of time. But training such integrative movements is pivotal in inducing learning transfer from motor patterns to autonomic functions that resulted in the cure of urinary bladder function.