Here's what I know so far...it'snot much and it's not 100% confirmed either.
MGS3 Home
It is the 1960's...the cold war ensues.  Our hero...Naked Snake AKA Big Boss has been sent to stop an evil organisation know as Cobra. (I know it sounds like G.I.Joe.)
Game Dialogue
Cast of characters:
Big Boss lives!
Naked Snake AKA Big Boss (Naked means no equipment not no clothes.)
Real name is Jack.  He is a member of FOX (Force Operations X) the special operations team that later becomes Fox Hound. 
The Boss
Revolver Ocelots mother.  She is Snake's mentor and true love.
Eva
Eva is a spy who poses as Sokolov's lover.  She is also romantically involved with Snake.  Snake does not know about her double identiry. .
Major Zero AKA Major Tom
He is Snake's main contact by radio during the mission.  He belongs to the CIA bereau of planning and the commanding officer of FOX
.
Mr. Signit
Mr. Signit plays a simular role to that of Mei Ling in this game.  He gives Snake information on weapons and and advice on how to defeat certain enemies.
Ocelot
This is a much younger Ocelot who is only in his teens.  Snake's enemy and biggest rival.  Hopes to get even with Snake for embaracing him in front of his subordinates.
The Pain
A member of Cobra.  He has the ability to command a large number of bees.  He keeps a queen bee in his backpack, to guide other bees behind him.  He throws bee hives like grenades and a swarm of bees explodes out of the hive.  He keeps a highly toxic bullet bee in his skull that he can fire from his mouth at high speeds.
The Fear
A member of Cobra.  His arms and legs are larger than the normal person.  He can climb trees like a spider and can travel through the forest between trees with rope. (spider web?)  He has a long insect like tongue and can grab things with it.
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