The Boss used to be known as The Joy, when she was a member of the legendary Cobra Unit at the end of the Second World War. They consisted of The Fear, The End, The Pain, The Fury, The Sorrow and The Joy. Together, they helped to end the war.
The Sorrow was The Joy's husband, and they had a baby son together, which The Joy gave birth to on the battlefield. This birth gave her a scar in the shape of a snake along her body as she had to perform an emergency caesarean section on herself. This child is later revealed to be Ocelot, the soldier who appears in nearly every game.
Her father was a member of the Wisemen's Committee and he told her of the corruption that occurred which in turn, split them and the Cobra Unit up.
 Metal Gear Solid 3: Snake Eater
The Boss initially appears to be Naked Snake's advisor, but it is soon revealed that she has defected to the Soviet Union. However, The Boss was working to obtain the Philosopher's Legacy for America. When Volgin launches a nuclear missile and the blame fell on The Boss, she continued her mission knowing that her innocence would only be proved when America killed her. This was accomplished by Naked Snake.
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