Lyndon Johnson initially resisted the idea of forming a federal commission to investigate John F. Kennedy’s assassination, preferring to allow the state of Texas to review what he called a “local killing.” But after learning that both the U.S. Senate and the House of Representatives were considering launching their own inquiries, the newly installed President assembled the Warren Commission in the hope of avoiding multiple and possibly conflicting reports on the shooting.

Johnson wanted the Commission to include members from each of the different branches of government, but many of his preferred choices were hesitant to participate. Wary of the possible legal entanglements of serving, Chief Justice Earl Warren turned down the opportunity to chair the commission multiple times, and only agreed after Johnson argued that an inadequate report could incite a public panic and even spark a nuclear war. Meanwhile, conservative Senator Richard Russell flatly refused to serve because he disliked Warren’s liberal judicial record. Johnson waived off Russell’s protests and publicly named him to the Commission anyway, saying his participation was necessary “for the good of America.”

While serving as a leading member of the Warren Commission, future U.S. President Gerald Ford also acted as an inside informant for J. Edgar Hoover and the FBI. Several months after his death in 2006, a cache of declassified documents revealed that Ford, then a U.S. congressman, had approached FBI Assistant Director Cartha DeLoach and offered to confidentially keep the Bureau informed on the Commission’s deliberations. Among Ford’s many leaks was the revelation that two unnamed members of the Commission—most likely Richard Russell and Hale Boggs—remained unconvinced by FBI evidence that the kill shot had been fired from the Texas School Book Depository.

Warren was a close friend of the Kennedy family, and his personal attachment may have interfered with his duties to the Commission. In one of the most infamous episodes of the investigation, Warren denied his fellow Commission members access to Kennedy’s autopsy photos because he deemed them too disturbing. He later refused to allow the Commission to interview certain witnesses whom Lee Harvey Oswald may have known in Mexico, and even tried to block an interview with first lady Jackie Kennedy because he didn’t want to invade her privacy.

Many believed that Fidel Castro might have conspired in Kennedy’s murder, and it turns out that the Cuban dictator personally proclaimed his innocence in an off-the-record interview with the Warren Commission. According to journalist Philip Shenon, at one point in the investigation, Commission lawyer William Coleman met face to face with Castro on a fishing boat off the coast of Cuba. During a three-hour exchange, Castro repeatedly denied having any involvement in the assassination. No notes were taken during the secret rendezvous, and only Earl Warren and one other investigator were ever made aware of it.

The FBI and the CIA had monitored Lee Harvey Oswald in the months before the assassination, but both agencies later tried to downplay their knowledge of him to the Warren Commission. Oswald had once even left a threatening note for an FBI agent at the Bureau’s office in Dallas. Fearful of catching blame for not preventing the assassination, the FBI later destroyed the note and even removed the agent’s name from a typewritten transcript of Oswald’s address book provided to the Warren Commission. Congressman Hale Boggs would later say that FBI Director J. Edgar Hoover “lied his eyes out” to the Commission’s investigators.

Evidence also suggests that the CIA had Oswald under surveillance when he made a trip to Mexico in September 1963 and visited the Cuban and Soviet embassies, but the agency repeatedly denied any connection to the alleged shooter. The CIA also neglected to inform the Commission about its many covert operations in Cuba—including several schemes to assassinate Fidel Castro—even though those revelations might have helped shape the investigation.

While the 888-page Warren report went into great detail outlining how Lee Harvey Oswald could have killed Kennedy, it gave little explanation of why he did it. In its findings, the Commission stated that Oswald’s actions could not be explained if “judged by the standards of reasonable men,” saying only that he was an isolated individual plagued by a life of failure and disappointment. The report would later conclude that, “the Commission does not believe that it can ascribe to him any one motive or group of motives.”

Although they praised the Warren Commission report in the media, many government leaders had serious misgivings about its findings. Commission member Richard Russell reluctantly signed the Warren Report even though he could not rule out the possibility of a conspiracy, and he later admitted to having “lingering dissatisfaction” with many of its conclusions. Congressman Hale Boggs had similar doubts about the report, in particular the “single bullet theory”—the argument that one shot had stuck both President Kennedy and Texas Governor John Connally.

Lyndon Johnson remained in lock step with the Warren Commission’s findings for most of his career, but he privately disagreed with the single bullet theory and reportedly believed that the Cubans had engineered the assassination. Likewise, President Kennedy’s brother, Attorney General Robert Kennedy, publicly commended the Warren Report even though he suspected a conspiracy had taken place.

When the Warren Report was first released to the public in September 1964, polls showed that only 56 percent of Americans agreed with its “lone gunman theory.” But within months, critics began to poke holes in its conclusions and methodology, and conspiracy theories cropped up alleging the involvement of everyone from the Mafia to Lyndon Johnson himself. By 1966, a second poll would show that only a meager 36 percent of people still had confidence in the report. Today, studies show that around two-thirds of Americans believe in some form of conspiracy surrounding the assassination.

After the public release of new information including the Zapruder film—an amateur recording showing the Kennedy assassination in shocking detail—the U.S. House of Representatives formed the United States House Select Committee on Assassinations and reopened the investigation on the president’s murder. In 1979, the HSCA stated that acoustic evidence from a Dallas police officer’s radio showed it was likely that two shooters had fired on Kennedy’s limousine, and it concluded that the assassination “probably” involved a conspiracy. Although subsequent investigations have cast doubt on the radio evidence, the HSCA’s report helped fuel public dissatisfaction with the efforts of the Warren Commission.