Well, after being forced to kill The Boss, and seeing how she was used and thrown away by the government she devoted her entire life away, disillusioned him. He broke away from the United States and formed his own military nation, to create a place where soldiers would always have a place. In time this desire devolved, as being surrounded by constant conflict and strife turned him into the warmonger he'd become.
From Metal Gear 2:
I never really felt like there was a need for Kojima to explain what happened between MGS3 and MG1, it always seemed like a natural enough route, but I did think maybe there was room to tell a story of its own in that time period, one that could be interesting for its own reasons.
Instead all we get is a bunch of dumb junk about mammal pods and wolbachia.