John was born 1930 in Maui, Hawaii, as a 3rd Generation Japanese-American. His mother died in childbirth, and his general childhood was a wartorn one, which culminated in the repercussions of the attacks on Pearl Harbor – he and his father were interned in the Sand Island War Relocation Center, Honolulu Harbor, from 1941 to 1945, due to his partly Japanese ethnicity. During the internment, John's father passed away, and most of his other relatives ended up being victims of war.
When he was released along with the other internees at the end of WW2, he'd been barely 16 years old and a war orphan. Having no other place to turn to and being unable to emigrate to Japan due to financial and language problems, he ended up enlisting himself for the United States Army (US Army Forces Command) for military service as a renaturalized US American.
He underwent Basic Combat Training at Fort Benning, Georgia, and Advanced Individual Training at the United States Army Chemical School, Fort Leonard Missouri, from 1946-48, being one of the best of his age group.
1950 John was transferred to the US Special Forces (Green Berets) and took part in the Korean War, and that's also where he first met The Boss, a legendary WW2 hero. Seeing the great potential in him, she decided to take him in as her disciple. He spent the next 9 years mostly at her side, and he also developed CQC (Close Quarters Combat) together with her.
In 1954, John was exposed to an atomic blast while being stationed on the American base on Kwajalein in the Marshall Islands. At the time the testing of the first airborne detonation of a hydrogen bomb took place at the Bikini Atoll, which had been nearby. He suffered the after effects and became infertile.
1959 was when he got suddenly separated from his mentor, The Boss, as she left overnight for a Top Secret mission. During that time he also took part in the Vietnam War with the Special Forces and met Python, a skilled soldier who he would befriend. The next few years he mostly spent serving as Green Beret, and occasionally working as a mercenary for various mercenary units.
It was not until 1964, when the FOX (Force Operation X) unit was established by a man called Major Zero, that he would finally meet the Boss again as he participated in FOX's first field missions, the 'Virtuous Mission' and 'Operation Snake Eater'.
Now assigned the codename 'Naked Snake', FOX sent Snake to Tselinoyarsk, Central Russia, to rescue weapons scientist Dr. Nicolai Stephanovich Sokolov and escort him back to the United States. However, the mission didn't go as planned - The Boss defected to the Soviet Union, working together with GRU Colonel Volgin, and took Sokolov with her.
Colonel Volgin also decided to fire one of the two miniature nuclear warheads The Boss had provided him with at Sokolov's Research Facility as they left, an action which led to Operation Snake Eater, taking place one week later.
Once again sent to Tselinoyarsk, it was now Snake's mission to rescue Sokolov, destroy the Shagohod (a giant tank capable of firing nuclear warheads) and eliminate Colonel Volgin and The Boss, now labeled a traitor, to prove America's innocence regarding the nuclear strike.
One of Snake's objectives also was to get into contact with an agent called ADAM, an ex-NSA codebreaker – however, at the meeting point, he met a female spy called EVA instead. Working together with her, Snake succeeded in infiltrating the fortress of Groznyj Grad, destroying the Shagohod, and eliminating Volgin, The Boss, and her Cobra Unit. He also received the 'Philosopher's Legacy' from her, a microfilm which held data of transactions of massive funds of cash amassed by the Philosophers, an organization originating from a secret pact formed between the US, China and Russia after WW1.
It was also during this time that Snake first met Ocelot, a triple spy at Volgin's side, working for the KGB, CIA and the Philosophers at the same time. From their first encounter on, Snake had begun to develop an immense amount of respect for Ocelot and his abilities, and vice-versa, despite the mans (faked) attempts to kill him (everything he managed to do was shooting Snake's right eye out by accident, resulting in his trademark eyepatch). When they fought for the last time in the WIG which would transport Snake and EVA safely outside enemy lines, Ocelot actually stole the Philosopher's Legacy from him, leaving him with a fake microfilm.
Snake returned back home to the US with EVA, who he had slowly fallen in love with. However, EVA turned out to be a spy for the Chinese government, and left him overnight, taking the fake Philosopher's Legacy with her and leaving Snake only an audio message with a confession.
It was then that Snake learned that The Boss had never truly defected to the Soviet Union, but that it had been her mission to locate and retrieve the Philosopher's Legacy and die at the hands of her own disciple, Snake, to prove America's innocence to begin with. However, she had not been allowed to tell anybody, and she would go down in official history as a war criminal.
With that in mind, Snake was awarded the title of 'Big Boss' by the US president, and called a true Patriot for all his efforts. Deeply hurt by all this, Big Boss quit the FOX unit and continued to work with different mercenary and counter-terrorist units like the Wild Geese and the Delta Force until 1969, while still serving the US Special Forces. He also found out about him being infertile during this time, and met child soldier Frank Jaeger in Mozambique, escorting him to an orphanage.
The San Hieronymo Incident, also called the FOX Unit revolt, took place in 1970. Big Boss had been captured by the unit, now going renegade in Colombia, South America, and they demanded to know where the other half of the Philosopher's Legacy was, and tortured him despite his lack of knowledge.
With the help of inmate Roy Campbell, a Green Beret, Big Boss managed to break out of the prison. He was able to get into contact with his old support team from Operation Snake Eater; Para-Medic and Sigint, who explained to him that the US Government held him and his former CO, Major Zero, responsible for instigating the revolt of the FOX Unit. In order to clear their names, Snake would have to stop FOX units leader, Gene, and take out the Metal Gear he had in development, dubbed Metal Gear RAXA.
In order to complete that mission, Big Boss and Roy Campbell had to persuade the Russian soldiers stationed at the base to join their ranks, including Frank Jaeger (now known as Null), who had been subjected to experiments by the Philosophers trying to create a perfect soldier; and Python, a former friend and comrade.
In the end, it was revealed that Gene actually wanted to launch a nuke at the Pentagon in America, not into Russia, in order to eliminate what was left of the Philosophers, whose last member had died in the 1930s. Big Boss foiled his plans and killed him, but received a microfilm containing all funds, equipment and personnel for 'Army's Heaven' from him; a nation of and for soldiers Gene had wanted to create.
Once again succeeding in his mission, Big Boss returned to the United States, greeted by his old CO, Major Zero. Around one year later, Big Boss would establish high-tech Special Forces unit FOXHOUND to continue the traditions of Zero and his now disbanded FOX unit. Around this time he also took up on the offer to form a new organization to replace the Philosophers, called The Patriots, with its founding members being their leader Zero, Ocelot, Para-Medic, Sigint, EVA and Big Boss. Their main goal was to carry on the will of The Boss, and to create a unified world state.
However, Big Boss soon realized that he'd only been a puppet to Zero all along (who'd also planned out both Operation Snake Eater and the FOX unit revolt), the opinions and interpretations of the two men began to clash, and arguments within the organisation arose. Zero wanted to deify Big Boss, the last apprentice of The Boss, and fearing that Big Boss would drift away from the organization, they carried out a secret project in 1972 called 'Les Enfants Terribles'. The intent behind the project was to clone the legendary soldier Big Boss, and thus Solid, Liquid, and Solidus Snake were born, with EVA serving as the surrogate mother.
Enraged by this, Big Boss left The Patriots and FOXHOUND and drifted from country to country for approximately the next 20 years, working for the Green Berets and as combat instructor, and helped to reintegrate former child soldiers back into society. He even became a minor media celebrity for a little while, and during the 80s he began to establish a fortress nation called 'Outer Heaven' in secret, located in South Africa, using the money he had obtained from Gene in order to create a haven for soldiers free from government control and to oppose The Patriots, who by this time already controlled the war economy and most of the worlds other cultural, financial and economical aspects.
Anticipating a counterstrike by The Patriots, Big Boss used his fame and reputation to return to FOXHOUND as its commanding officer in the 90s. Solid Snake also joined FOXHOUND during this time, unaware of the fact that Big Boss was his father, and became his student and subordinate.
Around 1995 Outer Heaven became fully operational, and Big Boss began to carry out his coup d'etat. He abducted Russian scientist Dr. Pettrovich Madnar, forcing him to create a new Metal Gear, and recruited dozens of skilled mercenaries from all over the world for his military nation.
With Outer Heaven posing more and more of a threat, Zero, unaware of Big Boss's plans, ordered FOXHOUND to sent an operative into the fortress to investigate – Gray Fox, formerly known as Frank Jaeger and Big Boss's most trusted ally. He ended up being captured, but revealed the existence of Metal Gear. Solid Snake was the next man Big Boss sent in, while providing radio support to him. Continuously trying to make him fail his mission and return to Zero with false information, Big Boss had not anticipated that Snake, a rookie, would actually make it this far. With the help of the local resistance members, Snake rescued Dr. Pettrovich Madnar, destroyed Metal Gear, and eventually took down Big Boss, the man behind Outer Heaven, who revealed to him with his last dying words that he was actually Snake's father.
The fortress was wiped out by the self destruct mechanism and an air strike issued by The Patriots, but with the help of Gray Fox and Dr. Pettrovich Madnar, Big Boss was able to survive, albeit crippled. Thanks to the Snatcher Project he was revived, his missing limbs replaced by artificial ones. He helped rescuing the local resistance members and fled to central Asia, together with his two allies.
4 years later, in 1999, Big Boss established the military state Zanzibar Land, similar in concept to Outer Heaven. FOXHOUND, with Roy Campbell now in charge, once again sent Solid Snake in to dispose of Metal Gear, rescue Dr. Kio Marv, and take down Gray Fox and Big Boss.
Being left in a state near death, Big Boss's body was recovered by The Patriots. They used nanomachines to induce a coma and keep him in a biomort like state for the next 15 years. This enraged both Ocelot and EVA, who'd secretly been working against The Patriots and for Big Boss while still being official members of the organization, and they finally left them completely, wishing to free Big Boss from his prison and end The Patriots' rule. They succeeded in retrieving Big Boss's body and replaced his missing body parts with ones from his other two dead clones, Liquid and Solidus.
It was not until the destruction of JD in 2014, the core of an AI which Zero had created to maintain world order, that Big Boss awoke from his coma. By this time, most of The Patriots' founding members had passed away already – only he and Zero were left.
Now able to learn the location of him, Big Boss brought Zero, a vegetable by that time, to the gravesite Solid Snake was visiting. Finally explaining the whole story to his son and making peace with him, Big Boss shut down Zero's life support, and willingly let himself be infected by the FOXDIE virus (a retrovirus which kills only specific people by simulating a heart attack) Solid Snake was carrying inside him, knowing it was programmed to target his genetic pattern.
Supported by his son, Big Boss finally died peacefully at the grave of The Boss, his mentor, the woman who taught him everything, while he admitted to his sins.