“JFK was on terrible terms with the CIA and the Joint Chiefs. He had refused to support the CIA organized Bay of Pigs invasion of Cuba. He had rejected the Joint Chiefs’ ‘Operation Northwoods,’ a plan to commit real and faked acts of violence against Americans, blame Castro and use the false flag events to bring regime change to Cuba. He had rejected the Joint Chiefs case that the Soviet Union should be attacked while the US held the advantage and before the Soviets could develop delivery systems for nuclear weapons. He had indicated that after his reelection he was going to pull US troops out of Vietnam and that he was going to break the CIA into a thousand pieces.”
http://www.paulcraigroberts.org/2013/11/21/kennedy-assassination-november-22-1963-50-years-later/