he year is 1970, six years after Operation Snake Eater. Snake, who doesn't use his real codename Big Boss as he doesn't yet feel that he deserves the title, is captured by his own unit, FOX, which has broken its allegiance with the CIA and captured a secret base in South America. In jail, he meets Roy Campbell, the sole survivor of a Green Berets team sent to investigate. The two escape and find out that both Snake and his former CO, Major Zero, are suspected of treason. The only way to clear their names is for Snake to stop the revolt and apprehend its leader, Gene.

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