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Conspiracies are one of the main themes of Deus Ex, and the game draws heavily upon popular real world conspiracy theories for many of its plot elements. These include speculations regarding black helicopters, vaccinations, and FEMA, as well as Area 51, the ECHELON network, Men in Black, cow mutilations, chupacabras (in the form of "greasels"), and Greys. Mysterious groups such as Majestic 12, the Illuminati, the Knights Templar, the Bilderberg Group and the Trilateral Commission also either play a central part in the plot, or are alluded to during the course of the game.
During sections of the game where the New York skyline is visible in the background, the two towers of the World Trade Center are noticeably missing; the real towers were destroyed a year after the game was released. Harvey Smith has explained that due to texture memory limitations, the portion of the skyline with the twin towers exists in the game's data files but had to be left out of the final game, with the other half mirrored in place of it. According to Smith, during the game's development, the developers justified the lack of the towers by stating that terrorists had destroyed the World Trade Center earlier in the game's storyline.[34]