The CIA, while not officially charged with investigating the assassination, was immediately involved due to Lee Harvey Oswald's purported visit to Mexico City, the photo surveillance and telephone tap surveillance surrounding that visit, and the subsequent charges of Communist conspiracy emanating from witnesses and officials in Mexico City.

The CIA's 201 ("personality") file on Oswald, quickly expanded into a general assassination investigation file, comprises the bulk of CIA holdings on the assassination. Documents released in the 1990s show the Agency deeply involved in the stories of Communist conapiracy which swirled out of Mexico City in the assassination aftermath, sometimes dampening them, other times enflaming them. Peter Dale Scott had called these "managed stories," and the CIA was the manager.