Phantom pain, also known as phantom limb, is a medical condition where an individual perceives to feel pain in limbs and organs that are not physically part of the body. Most amputees are known to suffer from this condition.
Shortly after walking up from his coma in 1984, Venom Snake begun to suffer phantom pain as a result of losing his left arm. Initially, Snake was unaware that he was an amputee, but as he continued having lucid moments, Evangelos Constantinou, M.D. revealed X-rays detailing the injuries. This revelation caused Venom Snake to go in to shock and he had to be sedated by the nurse, Alexandra Pikrammenos.
After escaping the hospital in Cyprus, Venom Snake was given a bionic arm by Ocelot to replace the crude prosthetic hook used in the hospital. Snake commented that he could still feel his real arm and that he felt pain occasionally in his left fingertips, with Ocelot mentioning the term and that his brain still remembered his original arm.
When Kazuhira Miller was rescued from captivity in Afghanistan, Ocelot offered to give him a bionic arm and leg to replace the former's own missing limbs. Miller refused, wanting to keep the feeling of pain as a physical reminder of his desire for revenge.
Behind the scenes
Phantom pain, or phantom limb, is a real life condition that most amputees are known to suffer from at some point in their lives. There are ways to make the pain easier with the use of prosthesis or therapy such as mirror therapy to trick the brain into thinking the limb is still there to make the pain subside. It is the namesake for Metal Gear Solid V: The Phantom Pain.
Although not the same as the medical condition, several incidences of "emotional phantom pain" occur throughout The Phantom Pain. Venom Snake experiences hallucinations of Paz Ortega Andrade as part of his immense guilt for not being able to save her from the second bomb, and Skull Face's death being atypical of antagonists in the Metal Gear series was meant to leave the player with a sense of longing for a true conclusion. Despite getting revenge, the player is supposed to feel unsatisfied, left with a residual "phantom pain."