As more and more Americans reported UFO sighting in the early 50s, the military's official denial of the phenomenon became increasingly suspect. Such categorical denial quickly became as much a cause of speculation as the origin of the UFOs. In 1952, the U. S. Air Force gave in to the public pressure to "do something" about UFOs and created Project BLUEBOOK, an official Air Force investigation into such reports. Given its subject matter, BLUEBOOK soon came to be entirely, although secretly, controlled by Aegis. It was Aegis' intention to use BLUEBOOK as a smoke screen for Aegis operations and as a source for public disinformation.

To reduce the possibility of a link being discovered between Project BLUEBOOK and Aegis, the BLUEBOOK staff contained no Aegis operatives. BLUEBOOK was a legitimate and official Air Force project, although Aegis made certain that the personnel chosen for the project were predisposed toward skepticism of the phenomenon.

The primary instrument of Aegis' control over the BLUEBOOK was another Air Force project completely hidden from the public eye, Project MOONDUST. Project MOONDUST was created in 1953 and charged with "the retrieval and exploitation of crashed foreign spacecraft". Within top military circles, MOONDUST's stated purpose was the recovery and examination of downed Soviet and Eastern Bloc spacecraft and satellites, but the MOONDUST charter clearly made it responsible for the recovery of extraterrestrial spacecraft as well. For this role it was exploited heavily by Aegis, and was staffed almost exclusively by Aegis personnel. All UFO reports were filtered through Project MOONDUST before transmission to Project BLUEBOOK, and only those reports deemed of little significance or validity were passed on.

At the end of its study, Project BLUEBOOK concluded that there was in fact no substantial evidence to support claims that UFOs were anything but misidentified terrestrial craft, weather phenomena or hallucinations. The Project's report was widely accepted by the populace and proved quite effective at undermining the credibility of those UFO reports that followed.

As always, there were those who were not convinced by BLUEBOOK's investigations and who saw the final BLUEBOOK report as the disinformation it was. Many of these people investigated UFOs and related phenomena on their own, attempting to uncover the truth and form their own conclusions. The most dangerous of these truth-seekers formed civilian investigative groups to better share information and resources. Fortunately for Aegis, these groups were often much too eager to recruit new members for their own good. Aegis Cells had little trouble infiltrating the organizations, subverting what information they managed to uncover, and guaranteeing that they never got too close to important information. Many of these groups were much more interested in finding evidence to support their pet theories than conducting serious investigations. This made them ideal mouthpieces for Aegis lies, and further degraded the credibility of all such organizations.

One civilian organization stood apart from the majority. This group could not be easily dismissed given the credibility of its membership. In 1956, Navy physicist Thomas Brown founded NICAP, the National Investigations Committee on Aerial Phenomena, an Unidentified Flying Objects and related events study group. Although NICAP was a civilian organization and contained many well-known civilian UFOlogists, a disturbingly large number of members were retired Air Force and CIA personnel. The Aegis operatives who were monitoring the group became acutely aware that many of the NICAP members had secret agendas. The operatives learned that some NICAP members were reporting back to groups within the CIA and other Intelligence Community organizations. Other members seemed to be working for an organization or organizations that Aegis could not identify. Due to the extent of NICAP's infiltration by agents from outside organizations with unknown objectives, little of the data it managed to collect can be trusted. Also, Aegis' inability to identify all the organizations operating within NICAP made Aegis Prime more paranoid than ever. Despite all this, NICAP served Aegis as a fertile ground for recruiting well-connected operatives and Cells.