After the death of the boss, Snake retired from the FOX unit, and the unit itself was mostly disbanded. However, during a revolt by members of the FOX unit in San Hieronymo-during which he and the other members of FOX were framed-Snake-who did not wish to fully adopt the title “Big Boss” yet-sprung into action. However, the exact nature of these events is not clear-due to “Portable Ops” having a sort of tricky place in the Metal Gear “canon”….what is known is that Big Boss shortly created the FOXHOUND unit as successor to the FOX unit, although he would shortly abandon it for years….
Shortly thereafter, using the funds from the Legacy secured during the rebellion, Big Boss, Major Zero, Ocelot, EVA and the other survivors of Operation Snake Eater formed a new group to help realize the Boss’s vision of a united world. Called the Patriots, or Cipher after Zero himself, they worked on several ways to make this happen.
However, eventually Big Boss’s ideal of a haven for soldiers “Outer Heaven”-and Zero’s view of the world being united through control-collided. Zero wanted to use Big Boss as an icon to draw people into Cipher. Fearing that Big Boss would leave, Zero asked Paramedic to create clones of Big Boss. Using DNA from Dr. Clark’s assistant as the “mother”, the embryos were then placed in Eva’s womb. Later, they were born-David and Eli, with a third, more ‘perfect’ clone Solidus being born through another method.
However, this made Big Boss even more angry, and he totally abandoned the Patriots and FOXHOUND, and in 1974, he formed the mercenary group Militaries San Frontieras in Columbia, co-led by fellow mercenary Kaz Miller. Starting with a few recruits, the size and significance of the group grew when they accepted an unusual contract-from a “Professor of Peace” (In reality a KGB agent) Professor Galvez and his “student” Paz. Their bait-an apparent tape-was a recording of what seemed to be the Boss, who had somehow miraculously survived Operation Snake Eater. They wanted Big Boss as well to investigate the mysterious group known as “Peace Sentinel” which were operating in Costa Rica-and bringing in nukes as well.
MSF took the job-in part because of the pleas from Paz. Galvez supplied them with an offshore facility, which eventually swelled to over 300 men and women. He quickly discovered that Sentinel-a somewhat rogue CIA unit-was developing a mobile walking tank weapon known as the Peace Walker, which was, in part, based on Granin’s “Metal Gear” ideas.
The voice heard on the cassette was in fact an AI pod used as part of Peace Walker’s “brain”, developed by Dr. Strangelove and Dr. Huey Emmerich. Strangelove was a colleague of the Boss’s, and blamed Big Boss in part for her death. MSF also teamed up with a group of Sandinista led by Amanda Libre, who also grew to admire Big Boss, and bailed him out of a hairy situation at a Peace Sentinel base.
After fighting various prototypes, Big Boss then confronted the Peace Walker itself which was on a buildup to launching a nuke, and after damaging it-but still about to fire-the unit submerged itself in Lake Nicouraga-successfully ending the nuclear threat, supposedly as the will of the Boss AI.
Snake took this the Boss giving herself up as a soldier; putting down her gun, and somehow rejecting his mercenary lifestyle. He vowed to not follow the same path, and threw away her bandana. He finally decided to accept the title given to him ten years before.
Big Boss: in the end, she put down her gun… and when she did… she rejected everything in her life up to that point, including me.
Kaz Miller:what do you mean?
Big Boss: in giving up her life she abandoned everything she was as a soldier…
Kaz Miller and you consider that betrayal…
Big Boss: I won’t make the same choice as her, my future’s going to be different…
yeah, that’s right… from now on… call me BIG BOSS!