Despite his apparent death in Snake Eater, it is revealed in Metal Gear Solid: Portable Ops that he survived and was put in a prison camp in Russia.
While imprisoned, the camp was secretly infiltrated by Gene of the FOX unit, who rescued Sokolov and succeeded in bringing him back to the United States and reuniting him with his family. While in the United States, Sokolov's previous assumptions came true, and he was recruited by Gene to design and build the first official Metal Gear project, based on a heavily modified version of the blueprints in Granin's office. Gene brought him to the San Hieronymo Peninsula to build Metal Gear RAXA and the ICBMG, while Sokolov secretly planned to rebel against Gene, who he had realized as a maniac.
When Naked Snake, now known as Big Boss, was captured by the remaining members of FOX, Sokolov saw his opportunity to rebel. After Big Boss escaped and began looking for ways to stop Gene's rebellion, Sokolov contacted him under the name "Prividyenie" (Ghost) . Ghost thanked Snake for taking care of Volgin six years prior, during the events of Operation Snake Eater.
After Big Boss destroyed RAXA, Sokolov emerged from the shadows and told him that RAXA was only a test model. Later, when Big Boss attempted to disable the ICBMG, Sokolov assisted him, telling where it's armor was at it's weakest. After the mission, Sokolov was presumably reunited with his family and retired from rocket science, for the better of the world.
