In the aftermath of Operation Pigeon Shoot's betrayal of its comrades in Operation Dove, The Watch splits into two distinct groups. The stated purpose of both groups was the protection of the human race from the predation of extraterrestrial and supernatural forces. Beyond that, the two organizations developed diametrically opposed.

The remnants of Operation Dove regrouped at Wright-Patterson AFB and set up a temporary center of operations. In an attempt to avoid a recurrence of the damage caused by Pigeon Shoot's treachery, a new organizational pattern was imposed. The new organization, modeled after the secret mystical societies of Europe, was composed of small independent groups or "Cells". The original founding group became the master Cell and selected members for the first generation of Cells. Each offshoot Cell had only a single contact to the "parent" Cell, whose true identity remained unknown. These Cells in turn recruited members into "child" Cells as necessary, and the process continued until an extensive network was established. The Cell structure minimized the information that could be revealed in the event hostile forces infiltrated or uncovered any particular Cell. Were this to happen, only the "child" Cell and its contact to the "parent" Cell would be compromised. The new organization, which continues to this day, was given the name Aegis, after Zeus' magic shield in Greek mythology. The Operation Dove members who formed Aegis' original "master" Cell came to be called Aegis Prime.

At the same time Aegis was forming, the members of Operation Pigeon Shoot started construction on a secret underground base in the New Mexico desert. This base was to become the research center and headquarters of a covert project within the U.S. military, answerable to no government authority and unknown to all but its agents and a few highly placed officials, who assured that any investigation was curtailed. The project was funded exclusively through the portion of the U.S. military budget assigned to covert or "Black" projects, leading the project's secret sponsor in the U. S. Senate to refer to it as The Black Book.

Despite the original common purpose of Aegis and The Black Book, the circumstances leading to the division of The Watch resulted in a great deal of animosity between the two organizations. This enmity was heightened as the Focus of The Black Book slowly drifted away from the protection of the human race and toward the acquisition of alien technology and knowledge by any means necessary. The Book's Military-Industrial Complex backers demanded concrete returns on their investment of time, power and monies. To this end, The Book began making deals with extraterrestrial; working with them, rather than against them. Over the years, the alliance between The Black Book and both the Greys and the Saurians grew very powerful. Aegis took a much harder stance on human-alien communication, in response to the disastrous results of Operation Dove. Because of the close ties between the extraterrestrial and The Black Book, Aegis came to view The Black Book as just as much of a threat as the aliens themselves.

The 1950s were an important period of growth for Aegis. Strong ties within the American intelligence community allowed Aegis Prime to create a number of powerful first generation Cells. These Cells were composed of high ranking officers from various agencies, giving Aegis Prime access to a large pool of information and resources. These Cells formed the backbone of the Aegis organization and established a strong foothold in the military and intelligence community, in particular the newly created U. S. Air Force and Central Intelligence Agency.