Now if you thought losing her parents, child, and the ability to have another child was big enough of a shit sandwich you ain't seen nothing yet.
This went on until 1959, when the never-ending cycle of The Boss getting recruited to do something and then immediately getting fucked over continued. The Boss was recruited by the President for a top secret plan that involved bribing Russian scientists and intellectuals that were against the Communist regime into handing over the secret plans of their space projects 'n' shit.
The CIA didn't want to help so The Boss used Philosopher spy channels to infiltrate the Soviet Union to accomplish this. The CIA then took the credit for this when the top secret plans started rolling in. Upon inspecting the plans being sent over and realizing something was fucked up, The Boss requested clearance for a mission to investigate. The CIA thought she was just assmad they stole her credit from her, so she infiltrated the Soviet Union again, this time alone with no support to personally find the guy who sent the plans, only to find out the CIA didn't even bother going through with paying the fucker. The CIA then blamed The Boss for this fuckup to avoid bad blood between them and the newly inaugurated JFK.
The Boss was then chosen for Project Mercury to see how the human body handles being in space. Her experience from nuclear radiation in Nevada meant that there wasn't much to lose if she got fried by space radiation. The test would've gone smoothly, but some bureaucrat told NASA to slap a window on the ship at the last second. During her flight, the view of the Earth from space inspired The Boss's idea that the world should be whole, united as one. At the end of the flight however, that very flight fucked up her re-entry and caused her to crashland. She survived, but was stuck in a coma for six months. When asked why their top agent was out of commission, the military lied and said she participated in the Bay of Pigs invasion and got rekt.
By the time she recovered, her spy in the Soviet Union was discovered by the Soviet Philosophers and was converted to a double agent by The Sorrow, who had returned to Russia. Because the spy had betrayed the US for reals this time and not because he didn't get his paycheck from the CIA, The Boss was sent in to neutralize both him and The Sorrow. If she didn't, then the Philosophers would kill her son.
The Boss and The Sorrow confronted each other on the bridge, talked about old times, and talked about which one would be the one to die. The Sorrow decided he should be the one to go, and so The Boss killed the closest thing she had to a husbando.
In late 1962, The Boss was contacted by Major Zero and under the authority of the CIA they formed Force Operation X, the FOX unit. Other members of the unit would come to include Donald Anderson, aka SIGINT, who would become the Chief of DARPA, Dr. Clark, aka Para-Medic, and John, now Naked Snake.
While all of this bullshit was going on, the СУКА that stole the Philosopher's Legacy was busy dying and passing over the microfilm to his son, Yevgeny Borisovitch Volgin, a colonel in the Russian GRU who wanted to overthrow Khrushchev.
Colonel Volgin used his limitless funds to build the military fortress of Groznyj Grad and fund the Shagohod project, which was only made possible by the brilliance of Dr. Nikolai Stepanovich Sokolov.
Dr. Sokolov grew to fear his creation, the Shagohod, a nuclear armed tank that can be deployed anywhere with three miles of flat terrain to allow it perform a rocket-boosted phase to launch an ICBM, and he defected to the West. His family was able to get out, but as a result of the Cuban missile crisis one of the Soviet Union's secret demands was that Sokolov be returned to them. The US did not know about the Shagohod yet so they complied. But in 1964, a mole working for The Boss revealed that the Shagohod project was nearing completion. And so the CIA decided it was time to retrieve both Sokolov and the Philosopher's legacy.
And here is where Metal Gear Solid 3: Snake Eater starts, with the Virtuous Mission as a dual attempt to retrieve both Sokolov and the Philosopher's Legacy.
Also the reason Major Zero is able to inform you of so many things is because he has covert XOF units on the ground whose only purpose is to remain hidden, monitor the mission, and provide intel.