I know a lot of anti-NWO folk like to say Kennedy was assassinated because of Executive Order 11110, but...
Why Three Kennedys Were Assassinated
National Security Memorandum No. 263, 11 October 1963
Pursuing Truth on the Kennedy Assassinations
I have never thought 11110 had anything to do with it. I would bet many who promote that theory have never even read 11110.
To me it was always about Vietnam, Cuba, and Russia. If I remember correctly, some of the Joint Chiefs at that time were promoting preemptive nuclear war against Russia. These were the same folks who dreamed up Operation Northwoods. Then there was the CIA's Bay of Pigs invasion.
I feel that by negotiating with Russia, planning a withdrawal from Vietnam, refusing to escalate the Bay of Pigs, firing Allen Dulles, etc., Kennedy angered too many people and sealed his fate.
Powerful people had been trying to get more control for a long time, and I am one of those who think that at least a partial coup of the U.S. government was accomplished with his assassination.