When this former government engineer involved in the construction of underground installations broke his security code and talked, alarm lit up the elite within the CIA and military who saw their personal escape hatch to avoiding the coming cataclysms closing. His death was not only to silence him, it was to send a clear and unmistakable message to any others who might be contemplating breaking their security oath. Should he have been found dead in an apparent suicide, the message would have been blurred. Thus he was gunned down, a simple engineer meeting a death that Mafia kingpins might meet, a death that would not be mistaken for a simple mugging or robbery. This worked, and most of the subsequent information leaks have been disinformation designed to cloud the facts so that the truth fades and begins to look silly alongside the company it must keep.
References to the Service-to-Self aliens the CIA had so quickly allied with are most often misunderstood, as where they were present in the underground installations, and where their technology was being examined by the military, the rules of engagement they were operating under are not understood by the populace hearing these tales. The military was warned not to tamper with certain devices, but proceeded anyway under the assumption that the warning was to keep them from knowledge, rather than harm. The orders to proceed endangered both the humans and aliens in the vicinity, but the Service-to-Self aliens cared only for their own safety and reacted in a manner that escalated into what has been interpreted as a shoot out. Each side thought they were defending themselves.
The alliance with Service-to-Self aliens occurred in the old days of MJ12, and matters are much different in the present day. MJ12 has come to the realization that they were lied to, and that the alien visitors come in two flavors, and have steadily migrated to an alliance with aliens in the Service-to-Other such as ourselves. Little of the old alliances remains today.