By 1999, the Cold War had thawed, and it seemed nuclear proliferation would soon be a thing of the past. Despite this, all was not well in the world. A series of shocks to the oil market spurred the development of new high-tech energy sources, including fusion power. However, most vehicles still relied on oil for power. Oil reserves were at a critical low, and the world community was prepared to take drastic measures, either by drilling into sand and shale for more oil, despite the difficulty -- or moving on to renewable fuels.
Such steps proved unnecessary when Czech scientist, Dr. Kio Marv, successfully bio-engineered a new species of algae, OILIX, that could produce petroleum-grade hydrocarbons with little expense and effort. Marv presented the algae to the World Energy Conference in Prague, and was on his way to a demonstration in the United States when he was kidnapped by soldiers from Zanzibar Land. NATO discovers that Zanzibar Land's leaders plan to hold the world hostage by controlling the supply of oil, and some good old-fashioned nuclear brinkmanship, courtesy of a stockpile of nukes.
Solid Snake was brought out of retirement by FOXHOUND's new commander, Roy Campbell, and is sent to Zanzibar Land to rescue Dr. Marv.