Why? The how and the who is just scenery for the public. Oswald, Ruby, Cuba, the Mafia. Keeps 'em

      guessing like some kind of parlor game, prevents 'em from asking the most important question,   

            why? Why was Kennedy killed? Who benefited? Who has the power to cover it up? Who?

The film opens first with newsreel footage including the farewell address in 1961 of outgoing President Eisenhower warning about the buildup of the military-industrial complex and then with a summary of JFK's years as President — emphasizing the events that, in Stone's thesis, would lead to his assassination — which finally builds to a reconstruction of the assassination on 22/11/1963. The film then switches to following New Orleans DA Jim Garrison as he learns about the president's death, and of potential links between the assassination and New Orleans. Attempting to help the government's investigation, Garrison and his team investigate the New Orleans links and bring in several potential accomplices, including private pilot David Ferrie, before being forced to let them go, as their investigation is publicly rebuked by the federal government. As suspected assassin Lee Harvey Oswald is himself shot on live television by Jack Ruby before he can go to trial, Garrison closes the investigation, but he still remains uneasy about what has happened.

The investigation is later reopened in 1966 after Garrison is encouraged to read through the Warren Report and notices what he believes to be multiple inaccuracies. He and other members of the staff interrogate several witnesses of the Kennedy assassination and others involved with Oswald, Ruby, and Ferrie at some point or another. Their first witness is Willie O'Keefe, a facist inmate serving five years in prison, who reveals he witnessed Ferrie discussing a coup d'état. As well as briefly meeting Oswald, O'Keefe was romantically involved with an enigmatic man called "Clay Bertrand." Another important person is teacher Jean Hill who witnessed some shots fired at Kennedy coming from the grassy knoll, and she states that upon giving her story, the SS threatened her into saying only three shots came from the book depository and nothing else. She proves this by revealing the changes to her testimony made by the Warren Comission during their "investigation" into the case. The D.A staff tests the single bullet theory by trying to aim an empty rifle from the same alleged window where Oswald shot JFK, but they also realize that Oswald was a poor marksman, indicating that the shots were fired by someone else, perhaps multiple marksmen.

Garrison secretly meets a shadowy high-level figure in Washington D.C. who identifies himself only as X and who suggests a conspiracy at the highest levels of government, implicating members of the CIA, the Mafia, the Military industrial complex, SS, FBI, and Kennedy's vice-president as co-conspirators with motives for Kennedy's assassination and/or the cover-up afterwards. X explains that the President was killed because he wanted to pull the United States out of the Vietnam War and dismantle the CIA. X encourages Garrison to keep digging and prosecute New Orleans based international businessman Clay Shaw for his alleged involvement in the conspiracy to murder Kennedy. Upon interrogating Shaw, the businessman denies any knowledge of meeting Ferrie, O'Keefe or Oswald, but he is soon charged with conspiring to murder the President.

As Garrison gets closer to his court date and case against Shaw, some of his staff begin to doubt his motives and leave the investigation when they start to disagree with his methods. Garrison's marriage begins to show signs of strain when his wife Liz complains that he is spending more time on the case than with his own family. Even his oldest son is convinced that his father does not keep his promises at family engagements. After a sinister phone call is made to their daughter, Liz accuses him of being selfish and attacking Shaw only because of his homosexuality. In addition, the media launch several broadcasts on television and articles in newspapers attacking Garrison's character and criticizing the way his office is spending the taxpayers' money on their investigation. Some key witnesses become scared and refuse to testify while others are killed, such as Ferrie, under suspicious circumstances. Before his death, a panicked Ferrie tells Garrison that "they" are after him and reveals there was a conspiracy around Kennedy's death, but he dies of an apparent suicidal overdose.

In March 1969, a jury acquitted Shaw of the charges after less than an hour of deliberation. The film reflects that members of that jury stated publicly that they believed there was a conspiracy behind the assassination but not enough evidence to link Shaw to that conspiracy. Shaw died of lung cancer in 1974 but five years later in 1979, Richard Helms testified under oath that Clay Shaw had been a part-time contact of the Domestic Contacts Division of the CIA.

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