During World War II, she established the Cobra Unit, where she was also known as The Joy, and on June 6, 1944 a pregnant Boss and her Cobra Unit took part in the D-Day invasion of Normandy. There on the battlefield, the Boss gave birth to her son while the father, The Sorrow, looked on. The child would be taken away by the Philosopher's and he would later grow up to be known as Revolver Ocelot. The Cobra Unit continued fighting in the war and would later be given the most credit for why the Allies won the war. After the war though, the Boss would disband the unit and each of it's members would scatter back to their own countries.

The Boss also began teaching a student and together they would develop a close quarters combat technique known as CQC. Jack, later known as Naked Snake, developed a deep attachment to her and he began to see her as a mother. The two spent ten year together before the Boss had to leave him to go on special missions.

On November 1, 1951, she became an atomic test subject as she took part in atomic testing in Nevada. In 1960, she was sent into space and once again was exposed to radiation. All of the exposure to radiation led to her being unable to bear children. In 1961, she was sent to Cuba to invade the country under the guise of taking Cuban exhiles back to the U.S. The U.S. betrayed them though, and the exhiles were killed by the Cubans. In 1962, she once again met her friend The Sorrow on the battlefield, but this time they were on opposite sides. There, at Tselinoyarsk, the Sorrow allowed her to kill him in order to complete her mission.

On August 24, 1964, The Boss pretended to betray the U.S. and defect to the Soviet Union in order to obtain the Philosopher's Legacy and destroy the Shagohad. In order to make the defection seem real, she also had to encounter her former student and nearly had to kill him. But Colonel Volgin fired an American made nuclear warhead and destroyed OKB-754. This leads the Premier of the Soviet Union, Nikita Khrushchev, to believe that the U.S. was behind the nuclear attack and demands proof that the U.S. was not involved. The Boss as well as the U.S. realize that in order to prevent an all out war they would have to send someone in to assassinate the Boss.