If you are referring to the "solid story" of the franchise (where .exe files for PC versions are sometimes discussed in modding communities), The Core Saga
Set during the Cold War, it follows Naked Snake (later Big Boss) as he is betrayed by his mentor, leading him to envision a world where soldiers aren't used as political tools.
The series eventually reveals that the world is controlled by a shadowy organization called The Patriots , who use advanced AI and nanomachines to manipulate global events and information. Common Characteristics of "Solid" Stories in this Context: