Phantom pain is what most amputees feel at the end of the remaining part of their amputated appendage. While the exact cause of phantom pain remains unclear, it seems to originate in the brain and spinal cord. During MRI and PET scans, parts of the brain that were neurologically connected to the appendage show activity when a person experiences phantom pain. Most experts believe that phantom pains can be explained partially by having mixed signals sent to the brain. The spinal cord and nerve endings no longer have input for the missing appendage and try to adjust in unpredictable ways. This can trigger the most basic signal for something not being right: pain.
Studies show that, because the missing appendage can no longer receive sensory information, the information is sent somewhere else; from a missing hand to a cheek that is still present. When that cheek is touched, it's as if the missing hand is also being touched. This is just another version of tangled sensory wires, so it can result in pain.
Other factors believed to cause phantom pain include damaged nerve endings, scar tissue at the amputation site, and the physical memory or pre-amputation pain.