I just picked up Jesse Ventura's book American Conspiracies, and one of the chapters explores the assassination of Malcolm X and how elements of the CIA/FBI set him up to die out of fear that he and Dr. Martin Luther King Jr. might form an alliance.
The official explanation of Malcolm X's death was that Black Muslims loyal to Elijah Muhammad killed him over a power struggle. Makes sense, right? Well there's more than meets the eye here.
Let's go back and explore what he was doing before his death. After his pilgrimage to Mecca, Malcolm dropped his hateful attitude and instead began forming alliances with revolutionary leaders in Africa and elsewhere, talking about civil rights as a human rights issue that the UNited Nations should take up.
By the time he returned to the United States on November 24, 1964, Malcolm had met with every prominent African leader and established an international connection between Africans on the continent and those in the diaspora.
The FBI had been keeping an eye on Malcolm as far back as 1950, and once J. Edgad Hoover (then director of the FBI) learned that Malcolm would be Elijah Muhammad's likely successor, one COINTELPRO file straight up said "The secret to disabling the [NOI] movement, therefore, lay in neutralizing Malcolm X." 
In 1958, John Ali was an advisor, friend, and housemate to Malcolm, and in 1963 became the National Secretary of the Black Muslims. When Elijah Muhammads health went south, John Ali took over handling the group's finances and administration. At that time he was also working closely with the FBI and keeping an eye on Malcolm .
Ventura then interjects some of his Navy training and comments on the Standard Operating Procedure that one would expect: "heavy surveillance to learn how you live, what way would be best to do it, how do we set up the patsy and get away with it?"
After Malcolm X was suspended by Elijah Muhammad for 90 days, the FBI seized that opportunity and unsuccessfully attempted to bribe him.
On March 8, 1964, Malcolm announced that he was leaving the NOI and founding a new mosque in New York. Shortly afterwards, he and Dr. King met in Washington and talked for the first time. Soon after that, King said that unless Congress moved quickly, they could expect that "our nation is in for a dark night of social disruption" .
At this time Malcolm headed off to Mecca, and while he was gone the NYPD's BOSSI (Bureau of Special Service and Investigation) was infiltrating his new mosque and passing information to the FBI and CIA. Anthony Ulasewicz was in charge of this operation, and he's known for being involved during the Watergate scandal . Ulasewicz brought onboard the black detective Gene Robers who joined up with Malcolm as a bodyguard . The cops/government were all over Malcolm at this point.
In late May 1964, the five guys who would assassinate Malcolm X met for the first time. They were a part of a paramilitary training unit, known as the Fruit of Islam, based out of Newark, New Jersey . That same summer, John Ali, the FBI informant from earlier, foreshadowed Malcolms death on a Chicago call-in radio station: "I predict that anuone who opposes the Honorable Elijah Muhammad puts their life in jeopardy." 
Malcolm was aware that he was being tailed by government agents, when he told a friend that "our Muslims don't have the resources to finance a world-wide spy network." . While dining in Cairo, Malcolm reckognized the waiter as a man he'd seen in New York, and he had to be rushed to the hospital to get his stomach pumped due to a toxin in his food. The waiter was long gone by then, but it was obviously a failed assassination attempt.
President Johnson passed down false information to Director Hoover, who then passed it down to Richard Helms, the man in charge of clandestine operations at the CIA. He authorized increased surveillance on Malcolm X even though the FBI told the CIA that the charges were trumped up .
Hoover wrote in a memo: "There are clear and unmistakeable signs that we are in the midst of a social revolution with the racial movement at it's core. The Bureau, in meeting its responsibilities in this area, is an integral part of this revolution." .
At this point Malcolm was aware that he had a target on his chest and was going to be killed soon. Despite repeated requests, the police would not protect him because he had a "bad [rap] sheet. You don't offer somebody like that protection." 
In 1965, Malcolm was frequently shadowed by potential assassins. John Ali waited for his arrival in L.A. along with a group from NOI, and 15 NOI members hung around outside his hotel in Chicago. When Malcolm wasn't allowed to enter France, journalist Eric Norden found out from a diplomat "that the CIA planned Malcom's murder, and France feared he might be liquidated on its soil." 
On February 14th, Malcolm's house was firebombed, but he and his family safely escaped. When a fireman left a gasoline bottle in his home to make it out to be a publicity stunt, Malcolm realized that the plots went much deeper than the NOI. 
By this time, Gene Roberts had become close friends with Malcolm, and had warned his supervisors of a potential attempt on his life next Sunday at the Audubon Ballroom, but apparently nothing came of it.
That Sunday, Malcolm X was assassinated in the Audubon Ballroom. Benjamin Thomas organized the killing squad, Wilbur X threw a smokebomb, William X shot Malcolm in the chest with a sawed of shotgun, and Talmadge Hayer and Leon Davis lit him up with pistol shots. Hayer was shot in the thigh, and when he made it outside he was beat by an angry crowd.
When Leon Ameer, a 32-year-old aide to Malcolm, went to the FBI 10 days after the assassination to talk about a conspiracy that included elements of the government, he was found dead a few days later in his Boston apartment. First it was ruled a suicide, then a drug overdose, and finally "natural causes." 
While the death of Malcolm X seems like a simple revenge killing, the it was clearly much deeper than that. The evidence shows that elements of our government were involved in his death.