The chance of some sort of conspiracy in the JFK murder case is not insubstantial. For all the attempts to close the case as "just Lee Harvey Oswald," fair-minded observers continue to be troubled by many aspects of eyewitness testimony and paper trails.

There remains the live possibility of a second gunman in the grassy knoll area. It is not just the number of Dealey Plaza spectators who believe one or more shots came from that locale. Who were the individuals representing themselves as Secret Service agents (with credentials good enough to fool Dallas policemen familiar with official identification) that appeared on the grassy knoll immediately after the shooting? The Secret Service has always insisted that the first agent to return to Dealey Plaza, Forrest Sorrels, did not do so until approximately 12:50 p.m. – a full 20 minutes after the presidential limousine came under fire.

The odds of conspiracy include a second possibility: There was no second gunman, but private assistance or encouragement was given to Oswald in achieving his murderous hit. The most likely suspects, based on the available evidence, would be the Mafia, the anti-Castro Cubans (who had an undisclosed cell operating in Dallas at the time of the assassination) or a small unsupervised cabal within the CIA. All three potential suspects had the means, motive, and opportunity to reach out to Oswald either as a lone assassin or in partnership with someone behind the picket fence.

[JFK: 50 Years Later]

Unfortunately, we may never know what really happened on Nov. 22, 1963. And that's chiefly because two separate government committees – the Warren Commission (1964) and the House Select Committee on Assassinations (1976-1979) – botched what was arguably the most important murder investigation of the 20th century. The Warren Commission overlooked key witnesses, ignored inconvenient facts and released its final report before all of the pertinent evidence could be gathered and analyzed. The CIA and the FBI also misled the commission and did not disclose critical information about many matters.

More than a decade later, the House Committee's controversial conclusion that Kennedy had "probably" been killed in conspiracy was based largely on a single piece of evidence – a crude police recording from Nov. 22 that supposedly captured the sound of gunfire. It did not, as we have conclusively proven in my book, "The Kennedy Half Century," with a major new scientific study.

The shortcomings of both committees, coupled with the U.S. government's refusal to release all of its assassination-related files a half century after Kennedy died, have made it difficult for honest researchers to uncover the facts surrounding JFK's death.

[Read More: The JFK Myth, 50 Years Later]

Yet 50 years later, we can see part of the truth clearly: JFK was a marked man. He came to power just as inexorable forces in American life were colliding in a way destined to produce social upheaval during his term. JFK's surfeit of enemies, racial turmoil greater than we had seen since the Civil War era, domestic tumult that unsettled millions, the clash between the anticommunist right wing and those willing to negotiate with the Reds, and most of all, a shockingly casual approach to presidential security based on utterly false assumptions made Kennedy appallingly vulnerable, an easy target for murder. Given all the factors threatening JFK's safety, even without Dallas, Kennedy would have been very lucky to have been found next to a successor on the inaugural stand come January 20, 1969.

