The second story in chronological order.

It's 2005. Solid Snake is taken out of his retirement to spy the Shadow Mosses Island. Merly Silverburgh was also there to support Snake in the mission. However, the missions wasn't easy at all. Snake's primary mission was to defeat Liquid Snake, who started the insurgency, and destroy Metal Gear Rex, a bipedal tank that can launch nuclear missiles. Plus, FoxHound soldiers were there to stop Snake. They were Crying Wolf, Psycho Mantis, Vulcan Raven and Decoy Octopus. In the middle of the mission, Snake discovers qur was part of the project Les Enfants Terribles and that is a clone of Big Boss, and Liquid. Naomi Hunter, a scientist who "helped" Snake, injected into the Snake FOXDIE virus, which kills only people with a particular gene, the gene of Big Boss. However, the virus does not kill Snake. In the end, Snake defeated the FoxHound, redeemed one scientist called Otacon, neutralized Metal Gear Rex and defeated Liquid, who died because of FOXDIE.

If you got any questions about the series, just ask it to me.