During the CIA's creation, Aegis Prime made certain that Aegis operatives were placed in key positions throughout the new organization. The newly commissioned agency was to become Aegis' primary powerbase in the intelligence community, complimenting the military resources gained through the similar "guidance" Aegis Prime provided to the fledgling United States Air Force. The CIA soon became Aegis' single largest source of operatives and information. The free reign given to the new agency by the U. S. government allowed Aegis operatives to work under the auspices of the CIA without fear of investigation.

Capitalizing on Cold War paranoia and rumors that Red China and the Soviet Union were achieving incredible results in their research into "brain-washing" techniques, the Central Intelligence Agency commenced research programs on mind control and human behavior modification. Aegis operatives monitored the programs, waiting to step in and take control of any that began to produce useful results. Should such results occur, the operatives would intercept and falsify reports to the CIA Inspector General so that only failure or very limited success would be revealed. In this manner, Aegis subverted any successful program's resources, and transferred the knowledge and further research to their benefit. Not all successful projects were "secured" by Aegis Cells, however. Some projects lacked properly positioned agents, others were just too distasteful. Still others were canceled without warning or explanation, or ended with the sudden disappearance or death of a key researcher. These mysterious events lead Aegis to conclude that at least some of the CIA's secret mind control projects ended up in the hands of The Black Book.

The fear of Communist superiority in any area provided a smokescreen and apparent motive for a wide range of behavior modification projects conducted by the CIA. Early projects such as BLUEBIRD and ARTICHOKE concentrated on a few specific techniques, most commonly mind-altering drugs, hypnosis and brain surgery. These projects resulted in some impressive successes, but the most ambitious and successful project by far was MKULTRA.

The MKULTRA Project was in fact several research projects combined into one. Widely disparate subjects were being investigated, such as psychoactive drugs, hypnosis, sensory deprivation, cerebral implants, microwave radiation, Extra Sensory Perception and brainwashing through cult indoctrination. Most of these topics had been studied previously, and MKULTRA broke little new ground in each field independently. What made MKULTRA so successful was its study of the interaction and combination of these varied disciplines. These experiments yielded the MKULTRA team two very impressive programs.

Through a combination of cerebral implants, psychoactive drugs and microwave transmitters, the MKULTRA scientists were able to create hidden split personalities. The test subjects were completely unaware of their condition and exhibited normal, obedient behavior until the introduction of a triggering stimulus, often via radio or microwave transmission. The triggering stimulus induced a trance-like state in which the subjects would carry out preprogrammed orders without hesitation or question. After the mission or task was completed, the subject would revert back to a normal state, completely unaware of actions taken while in the induced trance. These individuals were often used as covert assassins or couriers, unaware of their own role and therefore nearly undetectable.

MKULTRA's experimentation involving parapsychology led another research group to develop a strong psychic Warfare (Psi-War) program. These parapsychologists took individuals who showed an aptitude for extra-sensory perception and subjected them to a regimen of psychoactive drugs, hypnosis, sensory deprivation and advanced meditation techniques. The result was a group of powerful psychics capable of impressive feats of psychic power in several disciplines. Unfortunately, the treatments often left the psychics addicts, insane, or worse.

The Psi-War program in particular caught the attention of Aegis operatives within the CIA. They prepared to take control of the MKULTRA project by the usual means. Before this power shift could be fully realized, however, rumors of the MKULTRA project and specifically the Psi-War program found their way to the public and the news media. Public outrage caused a Congressional investigation during which the CIA downplayed the success of the program and emphasized that the subjects were all volunteers, which was not, in many cases, true. The investigation caused the official end of the MKULTRA project in 1963. But as was often the case, the project lived on, hidden from the public, and exempt from congressional inquires or other governmental accounting. The new MKULTRA project remains to this day wholly under Aegis control.