At this time, many new theories about the circumstances surrounding Kennedy’s death were introduced, among them the theory that three or four shots were fired and one of them was coming from in front of Kennedy, hence the common jokes about the "second gunman on the grassy knoll," and that there were Mafia connections between Jack Ruby and Lee Harvey Oswald. At this time, FBI and CIA involvement was first alleged to have occurred, and although the Committee dismissed such suggestions, they did conclude that the offices had destroyed evidence in the form of a note from Oswald. Many also feel that the film made by Abraham Zapruder was tampered with by a one of these agencies to prove that there was, in fact, one shooter, an allegation that he denies.

There is much controversy surrounding the actual bullets in John Kennedy’s body and if or how two shots could have both killed him and hit the Texas Governor Connally in the front seat. During Kennedy’s autopsy, four wounds were found: One large defect in the skull, one smaller one at the back of the skull, one in the throat, and one on the right side of the back. Without going very deeply into statistics, there was trouble judging the difference between the entrance and exit wounds, and the doctors did not take the time to discern the path of the bullet wounds through the body.

This has led to many references to the "Magic Bullet" theory, or the official version of the assassination published in the Warren report, that there was one bullet that caused all these wounds. These questions have also given way to criticism of the FBI and the CIA, who many feel, had tampered with, hidden, or even stolen crucial evidence in for a variety of motivations that we will discuss later. There are many small evidence thefts, all of which have been documented very thoroughly, in numerous different websites and books, but the most important ones are quite obvious.

After Kennedy’s autopsy was performed, his brain was placed in storage to be examined further at a later date. In 1966 when the materials surrounding his death and autopsy were moved to the National Archives for storage, it was discovered that his brain was missing along with other medical evidence including tissue, blood smears, and slides, along with photographs of certain areas of the President’s chest. Most people believe the President’s brother Robert Kennedy was responsible for this act as to prevent possible later attempts to desecrate his brother.

Since such pictures and materials were so closely guarded, it came as a great scandal when an agent of the CIA, Regis Blahut, broke into a closely guarded and monitored security room in 1978 and stole a folder of ballistics information, x-rays, and autopsy pictures. Although the CIA told the Committee that this act was one of "mere curiosity," it remains that specialists in fingerprint information say this was a deliberate act and that Blahut was primarily interested in pictures of the head.

Another incident that appears to be deceitful is on the part of the FBI, and it surrounds a Minox camera with a roll of film discovered in Oswald’s sea bag by the Dallas police department. As the story goes, Officers Gus Rose and Richard Stoval recorded the camera in a log and turned the evidence over to the FBI two days later when Agent Warren DeBrueys catalogued the bag and signed for it. Later the FBI contacted the two officers and told them that they had been mistaken, what was previously thought to be a camera was now recognized as a light meter. When they asked Officer Rose to change the invoice to state the camera was actually a light meter, he refused to do so, but on the official documents to the Warren Commission the camera was recorded as a light meter and the film had been exposed.

There is also a matter wherein the Senate Intelligence Committee was investigating CIA plots to murder Cuban leader Fidel Castro in 1975 and a correspondence from James Angleton to Assistant Director of the FBI William Sullivan, advising him to answer no to the questions "Was Oswald ever a CIA Agent?" and "Does the CIA have evidence of assassination conspiracy?" There is some evidence that agents were coached on their replies to questions surrounding the controversy.

Perhaps the most disturbing incident of all is the destruction of the U.S. Army file on Oswald that had been compiled before the assassination and not made available to the Warren Commission, along with a CIA file on Oswald. It leads to questions surrounding Oswald’s involvement in the CIA and why both the Army and the CIA had a file on him previous to his involvement in President Kennedy’s death, questions that need to be explored. Lee Harvey Oswald had a 201 file in the FBI records under the jurisdiction of Agent James P. Hosty opened December 9, 1960 in response to Oswald’s desire to return from an extended stay in the USSR where he had met his new wife, and there is also some suspicion that the FBI was very interested in him even before the opening of said file.

Marguerite Oswald went on record stating her belief that her husband was "an intelligence Agent of the United States government." There are others that back up this theory, claiming as former CIA finance officer James Wolcott does that Oswald was recruited by the military to be a double agent to the USSR. He claims that it was a stupid project and Oswald failed to convince the Russians of his loyalties, but that he was an agent nonetheless. In 1964 an investigation was conducted by a CIA representative John McCone who said that Lee Harvey Oswald was not an agent, employee, or informant of the CIA at any time. While there is very little that theorists about the JFK assassination agree on, there are connections that imply a strong link of some sort between the CIA, FBI and Oswald.

So why would the FBI and CIA want to hide their knowledge of Lee Harvey Oswald’s activities through a refusal to produce said records when the Warren Commission was looking for any and all documents pertaining to the death of President Kennedy? One of the many theories is that they had not informed the Secret Service of Oswald’s presence in Dallas, and as he was closely watched by both the FBI and the CIA, some see this as an attempt to kill President Kennedy simply by not protecting him.