It's not a standard evil Rooskies plot. In the prologue Big Boss goes in to extract a formerly defected Soviet rocket scientist, Sokolov, whose defection is actually the real reason for the Cuban Missile Crisis in MGS lore. The US handed him back to the Soviets to end the crisis but Big Boss (called Snake at the time) is sent to get him out after it turns out they are making him construct an advanced nuclear weapon.

The rescue goes wrong and a renegade Soviet colonel (who has lightning powers because MGS) steals Sokolov's weapon and blows up the research facility with a US-made Davy Crockett portable nuclear weapon that was given to him by Snake's former mentor who defects to the Soviet Union and promptly kicks Snake's ass.

Kruschev is furious about an American nuke detonating on Russian soil and demands the Americans go clean up their mess or WWIII is on the table so Snake is sent back to take out the renegade faction, Sokolov's weapon and his old mentor.

Of course, there's more plot twists and double crosses but it's not an average Hollywood dastardly gommulists affair