The Phantom limb phenomena is the feeling of pain in a limb that has been amputated or have lost function over a stroke.
The sensory units that are mapped to the amputated part are often remapped to other functions by the brain or spinal cord. Hence the areas of brain that had be coordinating the function of the missing limb become active and generates pain without receiving a sensory input from the limb.
It is the action of the brain and spinal cord in bringing about balance in its function.