The story follows a rookie FOXHOUND agent named Raiden, who is trained using virtual reality, as he infiltrates the Big Shell, an offshore environmental cleanup facility seized by a terrorist group called the Sons of Liberty. The group, led by a man claiming to be Solid Snake, holds the President of the United States hostage and threatens to destroy the facility, creating a potential environmental disaster. As Raiden and the player uncover the truth, they discover a vast conspiracy orchestrated by a powerful artificial intelligence network known as the Patriots, which manipulates global events and controls the world's leaders.

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