Footage of President Bill Clinton in the first few minutes of the film is not related to an official apology by the US Government for MK ULTRA experiments, rather for a similar project: The Tuskegee Experiments. The Tuskegee syphilis experiment was an infamous clinical study conducted between 1932 and 1972 by the U.S. Public Health Service to study the natural progression of untreated syphilis in rural African-American men in Alabama. The experiment's subjects were told that they were receiving free health care from the U.S. government.
At around the 50 minute mark, Thomas Blackburn (Ted Levine) mentions a story by H.P. Lovecraft about a scientist using radio waves to be able to see creatures from another dimension in his own dimension. The story he is referring to is "From Beyond", written in 1920 and published in 1934 in "The Fantasy Fan" magazine.