John (nicknamed Jack) was born in 1935, and joined the military in the 1950s, fighting in the Korean War. Jack met The Boss, becoming her protégé and disciple, and she taught him extensive combat, weaponry, survival, espionage, destruction, psychology, and foreign languages. In addition, Jack and The Boss later developed CQC (close quarter combat), which became a famous combat style.
Through the experience, Jack hold The Boss in high regard, viewing her as a mentor and parental figure in his life. In 1954, Jack was involved in the Bikini Atoll test of the first airborne detonation of the hydrogen bomb, and didn't develop the symptoms like his most of his friends, but was rendered sterile. On June 12, 1959, Jack and The Boss parted ways, and would meet again years later in Snake Eater.
In 1961, Jack was sent on covert operations during the early stages of the Vietnam War, and met and befriended Python. He later stated that Python was one of the few soldiers he could rely on during battles, and the two played poker together. The two were later involved in a mission where Python was shot and presumed dead.
Before 1964, Jack served in the Green Berets for several years, and became an experienced sniper in urban and marine environments. Also, Jack would eat snakes during previous survival training exercises, which would became useful during his future missions. Around this time, Jack was awarded various medals and commendations, including the Army Achievement Ribbon, the Good Conduct Ribbon, Defense Distinguished Service Ribbon, Korean Service Ribbon, the Distinguished Service Cross Ribbon, possibly the Vietnam Service Ribbon, and many others.
As revealed in a collection of prequels, John was originally a young FOX (a subdivision of the CIA) soldier and spy under the code-name Naked Snake. He was sent to assassinate his former mentor and spiritual mother, The Boss, in order to prevent nuclear conflict between Russia and the United States. After executing said task, as well as taking down Colonel Volgin and the Cobra Unit, he was left cold, unpatriotic, and bitter, having intense guilt and a burning urge to complete The Boss' original vision.
The Phantom Pain
After awakening in 1984, Big Boss was briefed on how the world changed in his absence. After discovering the plan to create a duplicate of him to act as a decoy, and take his place of the world stage until he was ready, Boss agreed to this plan. On 11th March, weeks after "Ahab" had awakened, and XOF beginning their attack on the hospital, Big Boss made his move. Posing as "Ishmael", he saved Venom from a female assassin, and claimed to be an ally who had "watched over him for the last nine years". During the escape Ishmael and Ahab encountered Tretij Rebenok and the Man on Fire. The hospital was then raided by a XOF strike force, and Ishmael saved Ahab from the XOF soldiers. While hiding among dead doctors and patients, they were caught by a XOF squad who were distracted and killed by the Man on Fire. Ishmael realized the Man on Fire's weakness, and shot the sprinklers, causing him to disappear. Ishmael and Snake recovered firearms from the dead XOF soldiers, and fought their way through the hospital.
Making their way to the entrance hall, Ishmael separated from Ahab to distract the soldiers, allowing Ahab to escape. After making it outside, Ishmael commandeered an ambulance and used it to run over the Man on Fire to save Ahab. Ishmael drove Ahab in the ambulance, evading XOF soldiers, but he was knocked unconscious after taking a shot from a helicopter. Subsequently crashing into a river bank, Ishmael recovered first and was pulled from the vehicle by Ocelot, leaving the unconscious Ahab. Ocelot returned to the base area to meet with Big Boss, who discarded the Ishmael role, and received a motorcycle from his ally.
Ocelot then gave Big Boss a U.S. passport and told him to go by the name in said passport and advised him to change his face, so he could secretly return to the US. Big Boss mused on the medic being his "phantom", before Ocelot assured him Ahab could handle it. After parting ways, Big Boss began his long term plan to create his new military nation: Outer Heaven. He used Venom Snake and his mercenary company Diamond Dogs to further the legend of his own name while working in secret. Sometime after Venom Snake regained his memories, Big Boss sent a cassette tape to Venom Snake, labelled "From the Man Who Sold the World," which revealed the truth, thanking Venom for his part in the deception.
In 1995, the USA learned of Metal Gear's development in Outer Heaven. As the leader of FOXHOUND with Venom Snake leading Outer Heaven, Big Boss commissioned FOXHOUND to infiltrate Outer Heaven and destroy the weapon before anyone else so he could buy Venom Snake time to finish the TX-55 Metal Gear. Big Boss sent rookie agent Solid Snake to save Gray Fox from Outer Heaven, and destroy the Metal Gear. Big Boss acted as Intel for Snake during this mission, but Snake proved to be far more competent than he realized, leading him to feed Snake false information.
Approaching the end of the journey, Snake discovered that Big Boss was secretly the leader of the very group who triggered the mission. He killed Venom Snake, unaware that this was Big Boss's "phantom", and destroyed the Metal Gear, with Outer Heaven being destroyed by self destruct. Big Boss used Venom Snake's death to fool the world into believing he was dead, and vowed revenge on Solid Snake.