Jumbo jet flight number 326 flying at an altitude of 35,000 feet gets hijacked by those unknown.
They have used the muscle relaxant Vecuronium Bromide -- a chemical that could be lethal if inhaled excessively.
Among the 517 passengers who are taken hostage in the cabin filled with Vecuronium Bromide is Senator Hach -- a man rumored to become the next United States President.

In the meantime on Lobito Island of the Moloni Republic in southern Africa... Inside the Lobito Physics and Chemistry Laboratory compound guarded by a mysterious armed force is a man standing.

His name is Solid Snake.

The hijackers of flight 326 are making only one request -- the handing over of "Pythagoras".
The United States work on identifying the hijackers and determining what the mysterious "Pythagoras" is and soon finds out that it is the name of a project on which research is conducted on Lobito Island.

The Moloni government is reluctant to cooperate, saying that it does not want any interference in its domestic affairs. Losing its patience, the US government sends in its special forces operation HRT, but the force gets attacked by the armed force there. All communications are lost.
With all of what is going on, contents of the classified research at the Lobito Physics and Chemistry Laboratory are about to be revealed.

With things in a deadlock, the US government decides to make use of its last resort -- the already retired legendary mercenary Solid Snake. There is not much time left till the time limit. Solid Snake's new battle begins at the secret lab on the mysterious and enchanting island.