Stone broke the film's structure down into four stories: Garrison investigating the New Orleans connection to the assassination; the research that revealed what Stone calls, "Oswald legend: who he was and how to try to inculcate that"; the recreation of the assassination at Dealey Plaza; and the information that the character of "X" imparts on Garrison, which Stone saw as the "means by which we were able to move between New Orleans, local, into the wider story of Dealey Plaza."  Sklar worked on the Garrison side of the story while Stone added the Oswald story, the events at Dealey Plaza and the "Mr. X" character.  Sklar spent a year researching and writing a 550 triple-spaced page screenplay and then Stone rewrote it and condensed it closer to normal screenplay length. Stone and Sklar used composite characters, most notably the "Mr. X" character played by Donald Sutherland. This was a technique that would be criticized in the press.  He was a mix of Richard Case Nagell and retired Air Force colonel Fletcher Prouty , another adviser for the film and who was a military liaison between the CIA and the Pentagon . Meeting Prouty was, for Stone, "one of the most extraordinary afternoons I've ever spent. Pretty much like in the movie, he just started to talk."  According to Stone,
Very well researched…just beautifully done!!! I met JFK Jr. 6 months before he was murdered and I told him him and we talked much about what you have written. JR. told me something at the time most did not know except those that killed him that he was going to run for president. He told me that he had 600 million in the bank,had a magazine called George and that he was going to tell the world who killed his father and he was going to run for president. NOW everyone would have voted for him to be senator and moved to be president and who had the most to lose…HILLARY and she became senator when she did not live in NY and now wants to be the first lesbian president and the darling of Wall street and the NWO.
One day at a country club in Manhasset NY soon after 9/11 , I met a man who was in his 70’s and said he ran the small business administration in Washington . He liked me very much and we talked about many things. I told him who killed JFK and why and then he said to me “Raymond I like you very much and I want you to know that I was JFK’S campaign manager and you are right but I want you to never repeat what you said because something might happen to you and you are a good person”