By the early sixties, Aegis had infiltrated every aspect of the government and was developing Cells in the private sector as well. Aegis had done a remarkable job burying itself within layers of government programs. The combination of the Cell structure and the HERMES network thoroughly concealed Aegis from public and government eyes. Even so, a not so insignificant incident in 1963 threatened to compromise the integrity of Aegis.

Through a routine illicit wiretap in the White House, President John F. Kennedy discovered that one of his own Secret Service bodyguards was an agent of some type of secret society called Aegis. After further surveillance by his own men, Kennedy discovered that his Secret Service agents were under the orders of this organization and were engaging in covert actions for the agency. President Kennedy confronted one of the agents and threatened him with a full Congressional investigation and imminent exposure. In exchange for his silence, Kennedy demanded that the agents make themselves available to him at any time to use as his personal covert operations team. The Secret Service Aegis Cell was caught completely off guard. They contacted their parent Cell and waited for instructions. The horrible answer was swift in coming. The parent's Cells mandate came directly from Aegis Prime. Kennedy must be eliminated. It would happen during his upcoming visit to Dallas.

Unknown to the Secret Service Cell or Aegis Prime, one of the Cell members was a double agent working for The Black Book. While Aegis was plotting the assassination, the double agent apprised The Black Book of the situation. The Book seized the moment and approached President Kennedy with a counter-proposition. The Black Book offered Kennedy protection from Aegis, and a group of agents to use as he saw fit, in exchange for Kennedy's assurance that any investigation in The Black Book's involvement with the Government would be silenced. Kennedy accepted the deal. The Aegis Cell recruited Lee Harvey Oswald, one of MKULTRA's success stories, for the dirty work. They supplied him with the details of the President's motorcade route and the buildings along the route whose security would be "overlooked" by the Secret Service. Unknown to Oswald, the Cell also positioned two psychics in the crowd outside the book depository as backup. Both psychics had powerful telekinetic abilities and were to insure that once Oswald's bullets hit, President Kennedy would be fatally wounded.

As the President's motorcade came into view, Lee Harvey prepared to take the shot. Suddenly, a Black Book agent burst into the room. Startled, Oswald hastily fired and turned to face the agent. Before The Black Book agent could bring his weapon to bear Oswald fired on him. The agent was wearing a bulletproof vest, but was stunned by the impact of the bullet long enough for Oswald to escape. The Black Book immediately tipped off the police, giving Oswald's description and general location. Oswald was captured within minutes.

Outside, Lee Harvey's shots hit the President, but off target. The Aegis psychics took over from there, bouncing the bullet through several vital organs in the President's chest. The damage was critical, but most likely not fatal. Yet, Oswald's attack was not the only one directed at the President at that instant. From a nearby grassy knoll, another assassin simultaneously shot the President, with a weapon quiet enough and powerful enough to blow Kennedy's head off. Although Aegis could not take credit, Kennedy had indeed been assassinated.

Aegis took two extremely important lessons from the whole episode, lessons which would change future Aegis operations. First, it was obvious that The Black Book knew about the plan beforehand. This increased Aegis' already excessive paranoia and forced them to regard The Black Book as a constant and lethal enemy never to be underestimated. Second, Aegis realized that they were not solely responsible for the Kennedy assassination. This again raised suspicions in Aegis of another secret group operating toward similar goals. The fact that the third party acted in a way helpful to Aegis did not dampen Aegis' concerns about this other group's motives. Aegis learned little more at the time despite intensive investigation, and in the end, Aegis simply counted the mission as an uneasy victory.