In 1991, Oliver Stone's movie "JFK" stirred up lingering questions about the Kennedy assassination, which happened 50 years ago this month. The movie rejected the conclusion of the Warren Commission, the official investigation that placed guilt on Lee Harvey Oswald alone; and instead, proposed a vast government conspiracy linked to the CIA.

The next year, in response, Congress created something called the Assassination Records Review Board, to set the record straight by declassifying material related to the assassination. The board released thousands of documents but as reporter Marcus Rosenbaum found out, that didn't settle much.

MARCUS ROSENBAUM, BYLINE: The first thing Jeremy Gunn says when you ask him about the Kennedy assassination is: I'm not a conspiracy theorist. I don't have a theory about what happened. But he knows a lot about it. He worked for the Review Board for four years, as its director of research and general counsel, and then its executive director. He read everything he could find in the government's files and questioned dozens of doctors and former officials, many of them under oath.

JEREMY GUNN: There were many things that were disturbing...

ROSENBAUM: And not just the well-known questions about the path of the bullet and where the shots came from, and Lee Harvey Oswald's odd travels. What really stuck out for him was the medical evidence - things like his deposition of James Joseph Humes, one of the doctors who performed the autopsy. Humes acknowledged that the autopsy was not performed strictly according to procedure. And then he said something else.

GUNN: Dr. Humes admitted that the supposedly original handwritten version of the autopsy that is in the National Archives is, in fact, not the original version.

ROSENBAUM: In a long statement, Humes spoke about taking his notes home the night after the autopsy, and remembering how he had once seen the chair Abraham Lincoln had been sitting in when he was shot, stained with Lincoln's blood. Here is an actor reading his testimony.

UNIDENTIFIED ACTOR #1: (As Dr. Joseph Humes) I thought this was the most macabre thing I ever saw in my life. It just made a terrible impression on me. And when I noticed that these bloodstains were on this document that I had prepared, I said: Nobody is ever going to get these documents. So I copied them, and burned the original notes in the fireplace.

ROSENBAUM: And those weren't just notes, he told Gunn. They were the first draft of the autopsy report.

GUNN: He had never stated that publicly to the Warren Commission. He had never been candid about that before.

ROSENBAUM: So Gunn asked him whether there was anything in the original document that was not in the copy. Humes replied, and I quote here, "I don't believe so." Then Gunn turned to another document. Here is the transcript of the questioning, read by actors.

UNIDENTIFIED ACTOR #2: (As Dr. Jeremy Gunn) Have you ever observed that the document now marked Exhibit 1, appears to have bloodstains on it as well?

UNIDENTIFIED ACTOR #1: (As Dr. Joseph Humes) Yes, I do notice it now. These were J's.

ROSENBAUM: He's referring to J. Thornton Boswell, another doctor at the autopsy.

UNIDENTIFIED ACTOR #2: (As Dr. Jeremy Gunn) Did you ever have any concern about the president's blood being on the document that's now marked Exhibit 1?

UNIDENTIFIED ACTOR #1: (As Dr. Joseph Humes) I can't recall, to tell you the truth.

UNIDENTIFIED ACTOR #2: (As Dr. Jeremy Gunn) Do you see any inconsistency at all between destroying some handwritten notes that contained blood on them, but preserving other handwritten notes that also had blood on them?

UNIDENTIFIED ACTOR #1: (As Dr. Joseph Humes) Well, only that the others were of my own making. I didn't - wouldn't have the habit of destroying something someone else prepared.

ROSENBAUM: After that, Gunn showed Humes the official autopsy photographs. Curiously, Humes had never handled them before; the Warren Commission had never shown them to him. Humes found it hard to tell what was what in the pictures.

Gunn says it's actually hard for anybody to tell what's what in those pictures, especially when it comes to such important details as whether Kennedy's wounds were entry wounds or exit wounds.

GUNN: One of the ways that we tried to sort out this story was to find the woman who had developed the original autopsy photographs. Her name's Sandra Spencer. She had never been questioned by the Warren Commission. But we located her.

ROSENBAUM: Gunn asked her to look at the autopsy photos from the National Archives. She didn't recognize them.

GUNN: She said: I didn't develop these. These are not the ones I developed.

ROSENBAUM: Here's her testimony, read by an actor.

UNIDENTIFIED ACTRESS: (As Sandra Spencer) The prints that we printed did not have the massive head damages that is visible here. The face, the eyes were closed and the face, the mouth was closed; and it was more of a rest position than these show.

ROSENBAUM: The official photographs seemed to be taken in a medical setting. The body was bloody. Spencer said the pictures she processed seemed to be taken in a darkened room with a flash.

UNIDENTIFIED ACTRESS: (As Sandra Spencer) They were very - what I consider pristine, for an autopsy. There was no blood or opening cavities, or anything of that nature. It was quite reverent in how they handled it.

ROSENBAUM: Here's something else. Gunn had asked her to bring with her some prints she had processed for the White House in the days before the assassination.

GUNN: So these would have been prints printed on, in theory, the very same paper that she had printed the autopsy photographs on.

ROSENBAUM: But the paper on the official photos didn't match the prints she'd brought along. They must have been printed at a different time, or a different place.

Now, Spencer was interviewed 30 years after the event, and that's a long time to remember every detail. But still, why didn't she recognize any of the official autopsy photos? Why are they on different paper from what she was using at the time? And whatever happened to the pictures she did remember processing?

Jeremy Gunn, who is now a history professor, can recite a litany of other unresolved mysteries surrounding the assassination, all questions that the Warren Commission failed to answer. Some believe that's all part of a cover-up, perhaps to hide a conspiracy that reached deep inside government itself. Others point to a more benign explanation. The new president, Lyndon Johnson, was pushing the Warren Commission to come to a conclusion quickly. He wanted to move forward, not look back. And besides, Gunn says, the panel genuinely believed that Oswald had killed Kennedy.

GUNN: And so they wanted to write the document in a way that would reassure the American public that it was a single gunman acting alone; somebody who's a little bit unstable, and that that's the explanation for what happened.

ROSENBAUM: The downside to that is, it looks like a whitewash when the facts aren't clear. But for the Warren Commission, transparency had its own difficulties.

GUNN: There are serious problems with the forensics evidence, with the ballistics evidence, with the autopsy evidence. And if they had - in my opinion, if they had said that openly, it would have not put the issue to rest.

ROSENBAUM: Faced with that, the Warren Commission went with what it believed. At first, nearly 90 percent of the public believed them. But within just a couple of years, that number was down to 36 percent and today, it's less than 25 percent.

Again, Jeremy Gunn.

GUNN: From my perspective, if the president had been killed as part of a conspiracy, that needed to be known. And wherever the consequences of that point, that should have been done. The institution that had the opportunity to best get to the bottom of this, as much as it was possible, was the Warren Commission; and they didn't do it.

ROSENBAUM: That's why 50 years later, this case has still not been closed in the arena of public opinion. And now, with nearly everyone having any connection to the events dead, all the unresolved mysteries surrounding the Kennedy assassination are likely to remain just that - unresolved.

For NPR News, I'm Marcus Rosenbaum.

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