In 2016, a jumbo jet carrying Senator Hach, an important politician and likely future presidential candidate, is hijacked by terrorists. In exchange for the senator, the terrorists demand Pythagoras, a research project being conducted in the Moloni Republic in southern Africa, from the United States government. In efforts to identify these terrorists, the government begins an investigation of Pythagoras.
The Moloni government refuses to cooperate and work with the United States, saying that it doesn't want to interfere in its current affairs. In response, the US sends in a covert special forces team to investigate, but the team is obliterated by armed resistance. With no other options and time running out, the US government calls Solid Snake to infiltrate the laboratory, discover the nature of Pythagoras and to rescue Senator Hach.
