Phantom pain

Phantom Pain, also known as Phantom Limb is a condition when an amputee can still feel the limb that is missing due to their brain still having the missing limb registered as still being there. Most amputees are known to suffer this condition.

History
Shortly after walking up from his coma, and escaping the hospital in Cyprus. Venom Snake was given a bionic arm by Ocelot to replace the crude hook that acted as a prothesis for his lost left fore arm. 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 remembers his original arm.

When Kazuhira Miller was rescued, Ocelot offered to give him a bionic arm and leg to replace those missing limbs. Miller refused, wanting to keep the reminder of the pain he feels from his missing limbs and the emotional pain of losing the original Mother Base and his comrades.

Behind the scenes
Phantom Pain, or Phantom Limb, is a real life condition that most amputees are known to suffer at some point in their lives. There are ways to make the pain easier with the use of prothesis or therapy such as mirror therapy to trick the brain into thinking the limb is still there to make the pain subside.