Metal Gear Solid 3: Snake Eater: A rescue mission for a defecting scientist named Sokolov goes wrong when a renowned soldier, The Boss, is revealed to be defecting to the Soviet Union. Her one time apprentice, Naked Snake, AKA Jack, is sent in to take her down and prove the involvement of the United Sates in a nuclear strike is false. Through defeating members of the now rogue COBRA Unit, Naked Snake also meets the double agent EVA, who aids him in ultimately defeating the newly designed Shagohod (a bi-pedal nuclear weapon) and the vile leader of the GRU soldiers, Colonel Volgin. The events lead to the final showdown between mentor and student, as The Boss and Naked Snake square off one last time. Naked Snake is awarded the title of Big Boss after the events of Operation Snake Eater, a title he refuses to call himself for several years.
Metal Gear Solid: Portable Ops: Six years following the events of Operation Snake Eater, Major Zero disbands the FOX Unit. Under the new leader, Gene, the remaining members of the FOX Unit capture Big Boss in order to discover the whereabouts of the Philosophers' Legacy. Big Boss, along with the help of a young Roy Campbell, eventually defeats the leaders of the rogue FOX Unit. Together, the two men lay the ground work for the operative group FOXHOUND. Big Boss also starts what would one day become "Outer Heaven."
Metal Gear: Gray Fox, a member of FOXHOUND, goes missing, and the commander, Big Boss, sends in rookie recruit Solid Snake to rescue Gray Fox, who is believed to be in "Outer Heaven." During the course of his mission, Solid Snake discovers Metal Gear, a bi-pedal nuclear weapon. Solid Snake is charged with destroying the weapon. Ultimately, he succeeds, but not without a price. Big Boss reveals himself as the man behind the "Outer Heaven" revolt, and Solid Snake fights his one time mentor to the bitter end. Big Boss ignites the self-destruct mechanism and seemingly perishes, at least until the end, when a message is delivered from Big Boss stating he would meet Solid Snake again.