The story of Metal Gear, in its entirety, begins with The Boss.
The Boss is a woman who, in her mid-20s, assembled a
cooperative special forces unit of american and soviet operatives in WWII that played a significant role in the allied victory (the "Cobra Unit".) Upon the start of the cold war, the Cobras were disbanded as her loyalties remained with the United States.
The Boss trained Naked Snake ("John," "Jack," "Big Boss".) for at
least a decade after WWII they were partners, and he was her last and
perhaps greatest apprentice. They were closer than allies, than friends
or family. In the late fifties they parted ways, Snake no longer her
fledgling but fully capable as an independent operative.
in 1964, in the height of the cold war, The Boss defected to the soviet
union, rejoining the Cobras under the ambitions of Colonel Volgin's
radicalist unit. There she gave her new hosts a pair of american-made
nuclear shells, along with the return of their asylum-seeking weapons
development scientist Dr Sokolov (the obligatory scientist-in-distress
of MGS3.) Unexpectedly, Volgin used one of these shells to eradicate a
soviet development site, removing evidence of his insurrections against
the soviet government and Premier Khruschev.
Naked Snake, her last disciple, was enlisted to find her and eliminate
her along with the growing soviet threat she has enabled. She never
expresses to him any purposes behind her defection, only that she is
'loyal to the end.'
Only in the end do we understand her purpose. only once snake's mission
is complete does he understand. The Boss's defection was, at first, an
order. She was to defect to the soviet union, specifically to Volgin's
command, as a ruse by the US government.