There are many plausible reasons why the CIA wanted JFK dead. 1) JFK knew the CIA was secretly countermanding all of his foreign detente efforts with the Soviet Union and Cuba, and Kennedy fought back. He acted like a real president, and the CIA did not like its power being challenged, especially after it had free reign over foreign and domestic policy under Eisenhower. 2) Kennedy kept defusing southeast Asia hotspots where the CIA was fighting a secret war. 3) JFK fired those sacred intel cows–Allen Dulles, Dick Bissell, and Charles Cabell–after the Bay of Pigs. 4) CIA cold warriors considered JFK a traitor (read JFK’s “peace” speech delivered at American U., June 10, 1963, for clarity on this point). 5) JFK wanted to “splinter the CIA into a thousand pieces and scatter it to the wind.” In short, JFK was at war with the CIA during his 1,000 days. Read my book for further proof of JFK’s knowledge of CIA covert/black ops. There was motivation aplenty for the CIA to do what it did. JFK bravely stood up to the bastards, knowing full well it was a dangerous game.