Metal Gear Solid 3: Snake Eater (Subsistence) 
Summary: In 1964, a special agent codenamed Snake is sent to Russian by the CIA, in order to rescue a scientist. He is being used to construct a nuclear weapon called the Shagohod, a tank-like machine which could start another World War. Snake defeats the Shagohod and his original mentor who was working with the enemy, and was given the title 'Big Boss' from his nation. 

Metal Gear/Metal Gear 2: Solid Snake 
Summary: In near-present time, a soldier is sent to take down a machine called Metal Gear, and faces off with the mastermind behind it; Big Boss. Big Boss supposedly dies, or at least has not been seen since. 

Metal Gear Solid (The Twin Snakes) 
Summary: Solid Snake is sent to stop another Metal Gear, and discovers the one in charge is some sort of blonde lookalike, named Liquid Snake. They are revealed to both be twins who were created as clones of Big Boss, in order to create 'The perfect soldier'. Liquid dies, Solid and his friend Otacon go off to live a normal life, for now. 

Metal Gear Solid 2: Sons Of Liberty (Substance) 
Summary: Snake and Otacon investigate a Metal Gear on a tanker, which is soon destroyed. Snake supposedly died in the explosion. Another agent is sent to rescue the president from a group who call themselves 'Sons of Liberty', his codename is Raiden. He goes through moments of doubt as well as being told that he is a pawn, but in the end the mastermind, another clone of Big Boss named Solidus, is killed, and peace is restored. 

Metal Gear Solid 4: Guns Of The Patriots (Yet to be released) 
Possible Summary: Liquid comes back in form of Ocelot, a rival to Solid Snake since Liquid was around. By now, Snake is of older age, and the world is in a depressing form of constant war. This story is, possibly, the end of the entire series.