Python was a war buddy of Big Boss during the Vietnam era who was originally a member of FOX. Python's unique FOX sneaking suit color was light blue. Python and Big Boss fought in Vietnam together, and after The Boss disappeared in the early '60s, Python was considered by Big Boss to be the one person he could count on in battle. However sometime during a secret mission in Vietnam, Python received a severe injury which cost him the ability to regulate his body temperature, and as a result, Big Boss presumed him to be dead. Without intense medical care, Python would overheat to the point where his body would literally burn itself up.
After recovering from his nearly fatal injury, he was trained by the CIA as an Anti-Snake soldier, the first of his kind. Python was genetically altered and trained to be Big Boss' exact match on the battlefield, so that in case Big Boss were to turn against the United States, the CIA would have a contingency plan to easily eliminate Big Boss as a threat. Due to his brainwashing and modification, Python grew to almost a sick obsession with perfectly matching Big Boss. To keep his abilities in check, he was regularly sent on wetworks assassination missions. Because of his wetworks assasination missions, he has had nightmares about those he killed, thus further driving him to kill Snake.
During the San Hieronymo Takeover, Python once again came face to face with Big Boss, but this time as his enemy. He explained why he has to kill Snake, and that he joined Gene's rebellion for his salvation. The two fought against each other, but Big Boss eventually gained the upper hand, and defeated him.
