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The main playable character in the first game, J.C. Denton, is a high-tech, nano-augmented agent for UNATCO. Although initially it is apparent that the organisation's genuine intent is to defeat global terrorism (which has manifested itself into a single body, the NSF, National or Northwest Secessionist Forces), it soon becomes clear that the director, Joseph Manderly, is infact taking payoffs from a sinister secret society bent on world domination, Majestic 12 (a splinter group, in the Deus Ex universe, of the Illuminati). As a consequence, it has become a tool for global hegemony.
UNATCO's US base is in the unlikely location of Liberty Island, although it is underground, presumably as not to spoil the view for tourists of the (now) headless Statue of Liberty. Even deeper beneath the base is a Majestic 12 laboratory, from which J.C. Denton must escape at one point in the game.