After the MJ-12 incident, Aegis Prime reevaluated its security measures. Two key aspects of the organization were deemed insecure: Aegis' base of operations at Wright-Patterson Air Force Base and its current procedures for distributing information. Wright-Patterson had attracted too much attention in recent years, resulting in rumors that 'Hangar 18' contained alien technology and extraterrestrial bodies. The rumors were correct, but the hangar number was wrong. Wright-Pat was just too close to population centers for proper security. A new base was needed, far away from prying eyes.

The methods Aegis used for distributing information between Cells was the other chink in Aegis' armor. Current procedures involved passing encrypted files physically between parent and child Cells. This was slow, relatively insecure, and required frequent contact between Cells. Aegis needed another way and new developments in technology provided it.

Both problems were addressed in a single, aggressive plan. Aegis constructed a secret military base, under the auspices of the Air Force, on the Nellis Bombing and Gunnery Range in Nevada. The Nellis Gunnery Range is a massive military base, roughly the size of Connecticut, used by the Air Force for live-fire tests and training missions. The detonation of munitions was not only accepted, but expected on the base. Aegis could deal with intruders and trespassing aircraft (terrestrial and otherwise) with whatever force deemed necessary, and blame training and testing operations for the gunfire and explosions.

The base was built on the shores of Groom Dry Lake and was designated a no-fly zone. On early flight maps the no-fly zone was marked Area 51, which became one of the base's many nicknames. Others included Dreamland, S-4, and The Groom Dry Lake Test Facility, but the base was given no official name or designation. Indeed, the military has no records of the base, and those officers who are aware of its existence are all members of Aegis. Aegis operatives simply call it The Ranch.

To alleviate the security problem inherent in distributing information through human connections, a massive computer system and database was constructed at the Ranch. This computer network, dubbed HERMES, became the repository for information gained through Cell investigations and research. Cells no longer needed to contact each other simply to relay information. HERMES also gave Cells a means of alerting Aegis Prime if their parent Cell was neutralized, preventing the Cell from being completely cut off. Each cell's connection to the HERMES network was provided by computer terminals specially manufactured at the Ranch for Aegis Cells. The main HERMES system was installed and went on-line before the base was completed. In time, The Ranch became a large research facility housing a myriad of Aegis research projects. Several Aegis Cells are based there, though none of them know who else on the facility is an operatives. The vast majority of researchers and workers at the Ranch are civilians and Air Force personnel unaware of the base's true purpose or commanders. The researchers work on small aspects of a project and never see its full extent. Those who do are either recruited into the Cell supervising the project or simply "removed".

The most prominent projects at The Ranch involve captured alien spacecraft. Most of the long term research centers around reverse-engineering extraterrestrial craft in order to exploit the alien technology. The most successful project to date in this area is the Aurora interceptor. The Aurora is a fantastic aircraft combining the best aspects of terrestrial aerospace technology, Atlantean cybernetic control systems and captured Saurian propulsion systems. The Aurora is one of the few craft at Aegis' disposal that has a respectable success rate for pursuing and overtaking alien craft. While six Aurora have been built, only four pilots have been found that can handle them so far.