Muhammad A. Aziz, one of two men wrongfully convicted of the murder of Malcolm X, said the decision to throw out the verdict against him 56 years after the assassination could not eliminate the decades he had lost.

“I do not need this court, these prosecutors or a piece of paper to tell me I am innocent,” said Mr. Aziz, who was released from prison in 1985. “I am an 83-year-old who was victimized by the criminal justice system.”

He added: “I hope the same system that was responsible for this travesty of justice also takes responsibility for the immeasurable harm caused to me,” noting that his wrongful conviction should have never taken place and was part of a broader trend “that is all too familiar to Black people.”

Thursday’s hearing came after a 22-month review of the convictions of two men, Mr. Aziz and Khalil Islam, in the 1965 murder of the civil rights leader. The review, jointly conducted by the district attorney’s office and lawyers for the men, concluded what historians and scholars had long argued: that the case against them was dubious from the start, based on conflicting witness testimony and no physical evidence.

“I regret that this court cannot fully undo the serious miscarriages of injustice in this case and give you back the many years that you lost,” said Ellen N. Biben, the State Supreme Court judge in Manhattan who presided over the hearing. As she granted the motion to throw out the convictions, the courtroom burst into applause.

The Manhattan district attorney, Cyrus R. Vance Jr., apologized on behalf of some of the nation’s most prominent law enforcement agencies before the judge’s momentous decision, which officially rewrites the narrative of one of the most painful moments of the civil rights era. He had submitted a 43-page motion written with the men’s lawyers asking that the convictions be vacated.

“I want to begin by saying directly to Mr. Aziz and his family, and the family of Mr. Islam, and of Malcolm X that I apologize,” Mr. Vance said as the hearing began on Thursday. “We can’t restore what was taken from these men and their families, but by correcting the record, perhaps we can begin to restore that faith.”

Mr. Islam, who spent more than 20 years in prison before being paroled in 1987, died in 2009, and those at the hearing lamented that he did not live to see his exoneration. Two of his sons, Ameen and Shahid Johnson, were gathered in the courtroom on Thursday, and tears welled in their eyes after the judge’s decision.

“I honestly didn’t think that I was going to live to see the day,” said Ameen Johnson, 57, in a brief interview outside the courtroom before the hearing began.

“It’s good but bittersweet,” he said, noting the absence of his father and mother. “They’re the ones who suffered.”

One of his lawyers, David Shanies, called Mr. Aziz “a dignified and brave man” who “suffered enough injustice for a thousand lifetimes” on Thursday, while expressing disappointment that Mr. Islam “never lived to see the day of his exoneration.”

“Nothing can give back these men or their families the decades of freedom that was stolen from them,” Mr. Shanies said, calling the two men victims of the same racism that Malcolm X spoke against throughout his life.

A third man, Mujahid Abdul Halim, was also found guilty, and his conviction stands. At the trial, he confessed to the murder but said and has maintained that the other two men were innocent.

The news on Wednesday that the convictions were expected to be thrown out spurred waves of reactions from the public, historians and civil rights leaders, who lamented the decades that Mr. Aziz and Mr. Islam spent in prison. The Rev. Al Sharpton called the miscarriage of justice “a strange and perverted irony.”

The wrongful convictions also allowed others to escape accountability, compounding the tragedy of a killing that silenced one of America’s most influential Black leaders — a man whose words and ideas still reverberate in contemporary social justice movements.

The men who some historians say were the actual assassins are dead, as well as the witnesses who testified and the police officers who handled the case.

Mr. Vance took up the case in January 2020, after meeting with Mr. Aziz and his lawyers from the Innocence Project and the office of Mr. Shanies, a civil rights lawyer. The “search for the truth” in the investigation was “severely impacted by the passage of time,” Mr. Vance said on Thursday, while apologizing on behalf of law enforcement.

On Thursday, Barry Scheck, the co-founder of the Innocence Project, called for officials to undertake “a larger investigation with greater access to evidence to get the history right.” He said that the suppression of exculpatory evidence by F.B.I. and police officials served to inflict “immeasurable” damage to the lives of the two wrongfully convicted men — and altered the record of a moment that still holds deep relevance five decades later.

“It would have changed the history of the civil rights movement in this country,” Mr. Scheck said.

A motion filed by the Manhattan district attorney asking a judge to toss out the convictions of Muhammad A. Aziz and Khalil Islam in the murder of Malcolm X concludes that crucial evidence was withheld during the men’s trial.

The 43-page motion, which was granted at a hearing on Thursday, described in detail the investigation conducted by the district attorney, Cyrus R. Vance Jr., and the men’s lawyers.

It concludes that if evidence withheld by the Federal Bureau of Investigation and the New York Police Department had been given to the defense, the trial would likely have gone differently.

“These defendants did not receive a fair trial,” the motion says. “And we respectfully submit that their convictions should be vacated and the indictment against them be dismissed.”

A New Witness

The motion includes a host of new findings. It mentions an interview with a new witness, J.M., conducted only days after the re-investigation began. J.M. said he was answering the telephone at the Nation of Islam’s Harlem mosque the day of the assassination and that his account backed up the alibi of Mr. Aziz.

“J.M. recalled receiving a phone call from Aziz at around 3:00 p.m. on February 21st, informing him that Aziz had just heard Malcolm X had been shot,” the motion says.

J.M. then hung up and went to get the mosque’s “captain” and together, the two men called Mr. Aziz back at his home.

“J.M. reached Aziz at home and told him the captain wanted to speak to him,” the motion says, a simple sentence that lends credence to Mr. Aziz’s story that he was at home at 3 p.m. when Malcolm X was shot.

A Trove of Documents From Law Enforcement

The motion details more than a dozen reports compiled by the F.B.I. and the N.Y.P.D. that were not disclosed to the defense, several of which point toward the men’s innocence.

The F.B.I. reports contain the accounts of several witnesses who describe gunmen who do not resemble the two men, as well as details about agency informants, who were present in the Washington Heights ballroom where Malcolm X was killed.

One F.B.I. report from Sept. 28, 1965, even contains a description of the man whom some experts on the assassination have concluded was probably the assassin who wielded a shotgun — William Bradley.

That report gives a description of Mr. Bradley, who was 27 years old at the time, that matches the one given by a defense witness of the shooter who had a shotgun.

“He had been a lieutenant in the Newark mosque and was known as a ‘strongman’ there,” the F.B.I. report on Mr. Bradley said. “He was a machine gunner in the Marine Corps.”

At least one of the witnesses at the trial was an informant for the F.B.I., according to the documents cited in the motion. One document, dated Feb. 25, 1965, said the bureau had ordered its local offices not to disclose to the New York police the fact that any witnesses were federal informants.

In addition, several F.B.I. reports indicated that, on the orders of the agency’s director, J. Edgar Hoover, informants were told not to disclose their relationship with the F.B.I. when talking to the New York police and prosecutors about the murder, according to a footnote in the motion.

The Police Department documents include descriptions of undercover detectives having been present in the ballroom, at least one of whom was there at the time of the murder. The report may have been referring to Detective Gene Roberts, an undercover officer who it later came out was working as a member of Malcolm X’s security detail.

Prosecutorial Misconduct

The report also describes prosecutorial files that included police reports that would have been helpful to Mr. Aziz and Mr. Islam’s defense. One noted that a witness in the ballroom who knew the accused men well had not seen them there but had seen other men who were associated with a Nation of Islam mosque in New Jersey.

The report makes it clear that prosecutors hid the fact that undercover officers were present during the shooting from the defense, a breach of the rules of evidence.

“The prosecutors were aware that undercover detectives were present at the time of the assassination,” the motion says, adding, “The People did not call any undercover officers at trial. There is no record of this information having been disclosed to the defendants.”

Because potentially exculpatory evidence never reached the defense, the re-investigation concluded that Mr. Aziz and Mr. Islam did not receive a fair trial.

The Question of Innocence

Though the trial was found to be unfair, prosecutors stopped short of declaring that Mr. Aziz and Mr. Islam were innocent of the charges. “Given the information currently available, the People make no determination on the question of the defendants’ actual innocence,” the motion said.

Mr. Vance was asked on Wednesday if he personally believed that the two men were innocent.

“Innocence is actually a term you won’t find in the penal law,” he said. “I will say this: The vacation of these convictions and the dismissal of the indictment means that they stand like any other person who has not been charged with a crime. They stand as presumed innocent.”

One of Malcolm X’s daughters said on Thursday that she hoped the exonerations of two men wrongly convicted of her father’s assassination would bring “a measure of peace” to their relatives, but that her own family was still seeking justice.

Ilyasah Shabazz was almost 3 years old when she watched her father get gunned down in an Upper Manhattan ballroom. On Thursday, she recalled her mother’s efforts to keep “the legacy and inspiration Malcolm brought to the world alive” after witnessing his “horrific” death — and demanded that those responsible be held accountable.

“Full justice will not be served until all parties involved in the orchestrated killing of our father are identified and brought to justice,” Ms. Shabazz, who is now 59, said in a statement. “It is our hope that finally the full truth can be learned.”

In the more than five decades since Malcolm X’s killing, the children of the civil rights leader — Attallah, Qubilah, Ilyasah, Gamilah, Malikah and Malaak — have pushed for answers along with other relatives, questioning the official narrative of the assassination and the role of government agencies in it.

Three of Malcolm X’s daughters were present in the Audubon Ballroom as gunmen poured bullets into their father and they say they continue to carry the trauma with them. As the shooting broke out, their mother, Betty Shabazz — who was pregnant with twins — threw herself over them, they have recalled.

Ilyasah Shabazz, who is the third oldest, said in 2005 that she has little recollection of the shooting. Still, she added at the time, “you still have to be traumatized by all the noise and commotion and my mother covering us up.”

For Attallah Shabazz, the oldest daughter, who was around 6, the image was clearer: “I’m a child with the forever memory of the most significant man in my life standing at a podium and falling backwards,” she said in a television interview in 2000. “That’s forever.”

The family has long been in conflict with Louis Farrakhan, the leader of the Nation of Islam, whom they accused of playing a role in the assassination plot, an allegation Mr. Farrakhan has denied. They also have sought to reframe the public understanding of Malcolm X’s legacy.

Ilyasah Shabazz’s 2002 memoir, “Growing Up X,” described her childhood and the memories she held of her father — and how her life was shaped by his own life story.

And Betty Shabazz, a civil rights advocate herself who died in 1997, said she taught their six daughters about their father by emulating his personality.

“I taught them about him by myself being disciplined and strict,” she said in 1993. “My children think my persona is me, when actually, it is their father’s.”

The exoneration of two men wrongfully convicted of the assassination of Malcolm X fueled questions on Thursday about the decisions made by the F.B.I. and its longtime director at the time, J. Edgar Hoover, during the investigation of the murder.

A motion to vacate the convictions, filed by the Manhattan district attorney’s office, said numerous F.B.I. reports were never disclosed to the defense, including some that discussed federal informants who were present in the ballroom where Malcolm X was killed.

The documents suggest the bureau, on Mr. Hoover’s orders, purposely kept information about its informants secret from the local authorities.

“We now have reports revealing that on orders from director J. Edgar Hoover himself, the F.B.I. ordered multiple witnesses not to tell police or prosecutors that they were in fact F.B.I. informants,” Mr. Vance said in court on Thursday.

The roles of the F.B.I. and Mr. Hoover in Malcolm X’s killing have come under scrutiny before. In 1964, one year before the civil rights leader was killed, Mr. Hoover wrote to the agency’s office in New York, asking it to “do something about Malcolm X,” according to one F.B.I. document released years ago.

The documents unearthed during the Manhattan district attorney’s review of the trial offered other new details. Four of the F.B.I. reports summarize interviews with a witness to the murder who had been a federal informant and testified at the trial, the motion said. It did not name the witness.

Another document, dated Feb. 25, 1965, said the bureau had ordered its local offices not to disclose to the New York police the fact that any witnesses were federal informants, the motion to vacate the convictions said.

Mr. Vance’s review found no evidence that the killing was orchestrated by the government. But it also did not answer broader questions about the role of the federal government and the police in the assassination.

An F.B.I. spokesman said on Wednesday that the agency cooperated with the Manhattan district attorney’s investigation but declined to comment on its outcome. Mr. Hoover died in 1972.

Still, the inability of investigators to resolve questions about the roles the F.B.I. and New York police played added to demands for a broader investigation into Malcolm X’s assassination, as the co-founder of the Innocence Project, which participated in the review, called for on Thursday.

The co-founder, Barry Scheck, said that the exoneration represented an official acknowledgment that the F.B.I. and police had “suppressed exculpatory evidence,” and that if they had not done so, “the history of the Civil Rights Movement in this country” would have changed.

Two men who were convicted of killing Malcolm X had their names cleared on Thursday. Here are five things to know about the assassination, and the developments over the decades.

1. In January 2020, a review of the case began.

Shortly before the release of a Netflix documentary series making the case the wrong men had been convicted, the Manhattan district attorney, Cyrus R. Vance Jr., ordered a review of the evidence against the two men, Muhammad A. Aziz and Khalil Islam. The investigation was conducted with the men’s lawyers, including the Innocence Project and the civil rights lawyer David Shanies.

Though many of the key witnesses were dead, the investigation was able to turn up a host of new details. One particularly revelatory interview came from a new witness identified only as J.M., an 80-year-old living in Brooklyn whose account supported the claim by Mr. Aziz claim that he was at home at the time of the shooting.

2. Malcolm X’s 1965 assassination came the year after he broke with the Nation of Islam

Malcolm X rose to fame in the early 1960s as the national spokesman for the Nation of Islam, a Black Muslim separatist group. Though he was considered a radical by much of the mainstream media at the time, he was a remarkable and persuasive speaker who described the way racism warped the lives of Black Americans.

In 1964, though, he broke with the Nation after bitter disagreements with its leader, Elijah Muhammad, prompting a host of death threats. A week before the assassination, Malcolm X’s house was firebombed as his wife and daughters slept inside.

3. One defendant confessed at trial and said that the other two defendants were innocent.

One man — Talmadge Hayer, who later changed his name to Mujahid Abdul Halim — was wounded and arrested at the ballroom, and within 10 days, two other men had been arrested: Mr. Aziz and Mr. Islam, then known as Norman 3X Butler and Thomas 15X Johnson, two members of the Nation of Islam’s Harlem mosque.

No physical evidence tied Mr. Aziz and Mr. Islam to the murder, and both men had alibis. And when Mr. Halim confessed to the murder on the witness stand, he said his two co-defendants were innocent. He repeated that in a sworn statement a decade later, naming four men from New Jersey as his co-conspirators.

4. New theories of the case emerged.

Over the years, evidence began to trickle out that suggested that Mr. Halim had been telling the truth. Still, the men’s attempts to overturn their convictions were rebuffed.

Support for them continued to build over the decades among experts on the assassination and in 2020, two landmark projects were released: One, a Netflix documentary series called “Who Killed Malcolm X?” assembled an compelling case in favor of the men’s innocence. And an award-winning biography of Malcolm X, “The Dead Are Arising,” offered a thorough theory of the assassination that pinned the blame on others.

5. The investigation found that the F.B.I. and the N.Y.P.D. had withheld crucial evidence.

But perhaps the most important revelations from the investigation were findings of evidence that had been withheld from the defense at trial, including documents from two of the nation’s premier law enforcement organizations: the Federal Bureau of Investigation and the New York Police Department.

Some of the F.B.I. documents never shown to the defense pointed away from Mr. Islam and Mr. Aziz. Prosecutors’ notes indicated that they failed to disclose the presence of undercover officers in the ballroom at the time of the shooting. And Police Department files showed that the police were aware a newspaper reporter had received a tip that Malcolm X would be murdered that day. There were few police at the ballroom that day.

The withholding of these documents raises more questions about how the authorities handled the case. But Mr. Vance’s investigation found that, had they been turned over during trial, there was a significant chance that Mr. Aziz and Mr. Islam would have been acquitted.

The men whose convictions in Malcolm X’s assassination were vacated on Thursday must have seemed like irresistible suspects to investigators who were searching for the assassins in 1965.

Muhammad A. Aziz and Khalil Islam, then known as Norman Butler and Thomas Johnson, were lieutenants in the Nation of Islam’s militia and worked at the Harlem mosque that Malcolm X had led before falling out with the sect’s leader, Elijah Muhammad.

At the time of the assassination, Mr. Aziz and Mr. Islam were out on bail on charges that they had beaten and shot a defector, Benjamin Brown, who had set up a mosque in the Bronx.

Those charges were later dismissed, but their status as Nation of Islam enforcers led the police to them in the days after Malcolm X’s assassination. Mr. Aziz, then 30, and Mr. Islam, then 26, were tried and convicted of the murder along with a third man, Talmadge Hayer, who later changed his name to Mujahid Halim.

Mr. Halim confessed to the murder on the witness stand but swore that Mr. Aziz and Mr. Islam were not involved. A jury convicted them anyway on the strength of testimony from several witnesses.

A decade later, Mr. Halim signed affidavits for his co-defendant’s appeal that identified four Nation of Islam members from New Jersey as his co-conspirators. But a judge dismissed his account and upheld the convictions of Mr. Aziz and Mr. Islam.

Mr. Aziz, who had served in the Navy, spent 20 years in prison before he was released on parole in 1985. Mr. Islam, who was once Malcolm X’s driver, was released in 1987. Both maintained that they had been framed by the true killers and whoever had ordered the assassination.

“They picked the right guy, because even if I felt I was going berserk watching myself get framed, they knew I would never talk, never give anyone up,” Mr. Islam said in a 2007 profile in New York magazine. “That was my mentality: straight up, what I thought was a righteous Muslim. The fact was, I was just the patsy. The perfect patsy.”

They served their sentences in some of New York’s most notorious prisons. Mr. Aziz was an imam at Attica before the 1971 riots; Mr. Islam was at Auburn when riots broke out in 1970.

In prison, both men changed their names and converted to a mainstream form of Islam, and Mr. Islam rejected the teachings of the Nation altogether. Mr. Aziz obtained his bachelor’s and master’s degrees in religious studies. He worked as chief of security for the Harlem mosque after his release.

On the outside, their personal relationships suffered in ways that outlasted their sentences. Mr. Aziz’s wife left him, while Mr. Islam asked his wife for a divorce. Their children — Mr. Aziz had six and Mr. Islam had three — were all younger than 11 when they were arrested and grew up without their fathers present.

“When I left them, the oldest was 5,” Mr. Aziz said near the end of a recent documentary series, “Who Killed Malcolm X?” He added, “I’m a father in name, I believe, only, not being there.”

Mr. Islam had overcome an addiction to heroin after finding a purpose in the Nation of Islam. He maintained until his death that he had nothing to do with Malcolm X’s assassination, though he said he saw it as inevitable.

“He was a sitting duck,” Mr. Islam told New York magazine. “Everyone’s got their destiny. He had his, I have mine. Our paths crossed, and we both suffered.”

The decision to throw out the murder convictions of two men in the 1965 assassination of Malcolm X represented a remarkable turn in the long-disputed case, but it also left larger questions unanswered:

What role, if any, did the Nation of Islam’s leadership play in the killing?

The F.B.I.?

The New York Police Department?

If the Federal Bureau of Investigation had as many as seven informants in the Audubon Ballroom, why were their accounts not fully shared with the Police Department, the prosecutors or the defense lawyers?

And if the Police Department had an undercover officer working in Malcolm X’s security detail during the assassination, why were his identity and account of events kept secret until 1970?

While partly clearing the two men, Muhammad A. Aziz and Khalil Islam, the 22-month investigation did not provide an alternative theory of the crime or clearly identify different perpetrators.

More broadly, the investigation did not attempt to explain why the nation’s largest police department was not able to protect Malcolm X when he was clearly in danger, or why the premier national intelligence organization, with blanket surveillance on Malcolm X and the organizations around him, was not able to see the attack coming.

Those questions, along with the weaknesses in the prosecution’s case, have captured the attention of scholars, filmmakers and amateur researchers and filled a shelf of books. But the justice system has not tried to answer them.

Instead, courts and the federal Justice Department have rebuffed calls for a full reckoning, most recently in 2011, after the Pulitzer Prize-winning biography by Manning Marable, “Malcolm X: A Life of Reinvention,” unearthed new evidence pointing to a Newark man as the likely prime assassin.

Last year, Les Payne and Tamara Payne, in their Pulitzer Prize-winning “The Dead Are Arising: The Life of Malcolm X,” published the most detailed account yet of the killing and the roles of the F.B.I. and the Police Department, including interviews with a Nation of Islam insider describing what he said were the group’s leaders’ orders to kill Malcolm X.

But the Manhattan district attorney, in the current investigation, was unable to identify this man.

The opportunity for a full reckoning gets slimmer with each year. Almost everyone involved in the case — the lead prosecutor and police investigators, the witnesses who testified at trial, the possible killers named in books and even Mr. Islam — are all dead.

One witness said he had been sitting near the front of the ballroom when one of the gunmen had sat down right next to him. Another said that same defendant was sitting in the 15th row. And a third witness said the gunman had been sitting somewhere else entirely.

The case against Khalil Islam and Muhammad A. Aziz rested entirely on eyewitness testimony. And yet, the eyewitnesses at their trial did not agree on what had taken place. Instead, the case produced a tangle of confusing, contradictory and inconsistent testimony about the roles the two men supposedly played in the assassination.

“It’s difficult to explain why the jury was convinced by this,” said Deborah Francois, a lawyer for the Shanies Law Office and one of the men’s current lawyers, noting that “there was not a single shred of physical evidence” connecting the two men to the crime scene, or to their co-defendant, known at the time as Talmadge Hayer.

The men were at a disadvantage though, given the resources of their adversaries at trial: the Manhattan district attorney’s office.

“Both of these men, they didn’t have resources,” said Barry Scheck, the co-founder of the Innocence Project, which worked alongside prosecutors to reinvestigate the case. “They were appointed public defenders and their public defenders were given a total of two or three thousand dollars to conduct their defense.”

Still, the prosecutors assembled a muddled case with a dozen eyewitnesses. The confusion extended to the guns that were used to kill Malcolm X. During closing arguments, the defendants’ lawyers noted that one witness, Cary Thomas, had testified before a grand jury that he had seen Mr. Islam brandishing a pistol but said during the trial itself that Mr. Islam was carrying a shotgun.

Mr. Aziz and Mr. Islam both offered alibis, which were backed up by testimony from their spouses, friends and others. But they had no apparent effect on the jury. And Mr. Halim, who initially testified he was not one of the assassins, took the witness stand a second time later in the trial to confess his guilt.

Then Mr. Halim told jurors that Mr. Islam and Mr. Aziz, who belonged to a Nation of Islam mosque in Harlem, were innocent and that three or four other men from a different mosque in New Jersey had been involved in the murder. He declined to identify them.

As the Manhattan district attorney’s office reinvestigated the case over the last two years, it found that the contradictions in the testimony only gave more weight to newly discovered evidence.

But 55 years ago, none of that seemed to matter to the jury. On March 11, 1966, all three defendants were found guilty and, a month later, were sentenced to life in prison.

Before Malcolm X’s murder in February 1965, there were attempts on his life in Los Angeles, Chicago and at his home in Queens, New York, all believed to be from members of the Nation of Islam. Mosques around the country, it seemed, were vying to be the one to kill him.

Scholars have focused on William Bradley, from Mosque No. 25 in Newark, as the man who ultimately fired the lethal shotgun blast.

Mr. Bradley, who died in 2018, denied he was involved. He was first identified by first name as one of the assassins in a 1977 affidavit by Mujahid Abdul Halim (previously Talmadge Hayer), who in 1966 confessed to being part of the team that killed Malcolm X.

A high school baseball star and later a Green Beret, Mr. Bradley was known as an enforcer on the Newark mosque’s muscle team, or goon squad. He served time behind bars for conspiracy, drug dealing and making “terroristic threats,” before being released in 1998.

Later, he turned his life around. He changed his name to Al-Mustafa Shabazz, married a prominent Newark civic leader named Carolyn Kelley, and appeared in a campaign ad for the Newark mayor Cory Booker, who went on to become a United States senator.

Few connected Mr. Shabazz to his past identity. Though William Bradley was a notorious strongman, Al-Mustafa Shabazz was a respected pillar of the community, working with children in his wife’s boxing center.

Then in 2010 an independent historian, Abdur-Rahman Muhammad, connected the two men and posted Mr. Shabazz’s former identity online.

He shared his research with Manning Marable, who published Mr. Shabazz’s name and tied him to the assassination in his 2011 Pulitzer Prize-winning biography, “Malcolm X: A Life of Reinvention.” Mr. Marable also speculated that Mr. Shabazz might have been an F.B.I. informant, either before Malcolm X’s killing or after, and that this brought him special treatment from authorities.

Though Mr. Bradley was known to the F.B.I. as early as 1963, his name never came up in the trial that sent Mr. Aziz and Mr. Islam to prison.

Either way, Mr. Shabazz continued to live openly in Newark. A 2015 article in the Daily News found him, at 76, driving a Mercedes and living in a pleasant neighborhood.

He denied any involvement with the assassination.

An interview with a new witness has added to the stockpile of evidence that prosecutors and defense lawyers have amassed to show two men who were found guilty in the assassination Malcolm X did not get a fair trial.

The witness, identified by investigators only as J.M., is an 80-year-old Brooklyn resident. And what he recalled of his experience on Feb. 21, 1965 — the day Malcolm X was shot to death — supports the alibi of one of the men who was convicted of the killing, Muhammad A. Aziz.

Mr. Aziz was a member of the Harlem mosque of the Nation of Islam who was known at the time of the shooting as Norman 3X Butler. He testified to the jury in 1966 that his legs had been injured the day of the shooting and that he was in such pain that he visited a hospital. He said he never went to the Audubon Ballroom.

Mr. Aziz told the jury that after he returned from the hospital, he was lying on the couch resting with the radio on when he heard a report about Malcolm X being shot. He then called his local mosque. After his call was returned, he said he spoke to a man he referred to as Captain Joseph about the murder.

Fifty-five years later, investigators interviewed J.M., who told them that he had been on “phone duty” at the mosque that day and had talked to Mr. Aziz about Malcolm X having been shot. J.M. said he then called Mr. Aziz at home, confirming that he was where he said he was, before handing the phone over to Captain Joseph, also known as Yusuf Shah.

According to investigators, J.M. told this story to a number of people over the years. His own daughter, who was present during the interview, had heard it several times. But his story had not made it into the official record of Malcolm X’s assassination.

In December 1970, an undercover New York City police officer was called to testify against members of the Black Panther Party who were charged with plotting to blow up buildings.

A defense lawyer asked the officer, Detective Gene Roberts, if he had helped to kill Malcolm X five years earlier. Detective Roberts said no, then stunned the court with his never-before-heard account of the assassination.

Detective Roberts, who had infiltrated Malcolm X’s security detail, testified that he was taking a break from guarding the front of the stage where the leader was speaking when the shooting started. He testified the assassins had been sitting in the front row, contradicting other witnesses and corroborating the account of the only defendant who confessed to the killing, Talmadge Hayer.

After shooting Malcolm X, Mr. Hayer fired a pistol at Detective Roberts and missed, the detective testified. Detective Roberts said he then threw a chair at Mr. Hayer, who was shot in the right thigh by another bodyguard, Reuben X Francis.

A photo of Detective Roberts giving mouth-to-mouth resuscitation to Malcolm X as he lay dying appeared in the March 5 edition of Life magazine. His police supervisors privately chastised him, but it is unclear whether they informed prosecutors handling Malcolm X’s assassination that the man who tried to save the dying civil rights leader was a detective.

The police had told prosecutors that there were undercover officers in the ballroom at the time of the murder, but prosecutors did not tell defense lawyers before the trial or call Detective Roberts to testify, according to the findings of a joint review of the trial conducted by the Manhattan district attorney’s office and defense lawyers. The fact that he was an undercover operative only came out when he testified against the Black Panthers.

His testimony would have been helpful to the other two defendants in the Malcolm X murder trial, Muhammad A. Aziz and Khalil Islam. Mr. Hayer, who later changed his name to Mujahid Abdul Halim, had testified that his co-defendants were innocent. This week the Manhattan district attorney, Cyrus R. Vance, Jr., agreed that the two had received an unfair trial and asked a judge to throw out their convictions, a motion that was granted.

“The fact that you had an active-duty New York City police officer there to corroborate that crucial detail of Hayer’s testimony is perhaps the most egregious violation that happened in this case,” said David Shanies, one of Mr. Aziz’ lawyers.

Several years after the Black Panthers trial, Detective Roberts signed an affidavit stating that he had no new information to offer that would help prove the innocence of Mr. Aziz and Mr. Islam. Their defense lawyers on appeal never interviewed the detective or tried to use his statements to support their case.

Detective Roberts moved on to routine detective work, and his supervisors transferred him to a quiet Bronx precinct when he developed an alcohol problem. He died alone in Virginia in 2008, though he was married and had a daughter.

Before his death, he told more of his story to Les Payne, an author whose biography of Malcolm X, “The Dead Are Arising,” was released in 2020.

In the book, Detective Roberts said that he had known Mr. Aziz and Mr. Islam from the Nation of Islam’s Harlem mosque, but that Malcolm’s killers were men he had never seen before. He had also warned his supervisors about a suspicious interruption at Malcolm’s speech six days earlier at the Audubon, which he believed was a dress rehearsal for the assassination.

“I told them I think it’s going to go down,” he said.

The warning went unheeded, he told Mr. Payne.

At the time of his death, Malcolm X was 39 years old and one of the most famous Black men in the world.

His rise to prominence was swift. He was first introduced to many Americans in a 1959 documentary in which he appeared as the national spokesman for the Nation of Islam. His rhetorical ability was fully on display as he emphasized the evils that white people had visited upon Black people and championed Black self-love.

The Nation of Islam’s leader, Elijah Muhammad, “teaches Black people to love each other,” he said. “And our love is so strong; we don’t have any room left in our hearts for hate.”

The year the documentary aired, he toured a number of African countries, including Nigeria and Egypt, where he met with President Gamal Abdel Nasser.

By the dawn of the 1960s, Malcolm X was a national celebrity, according to Les and Tamara Payne, the authors of the biography, “The Dead Are Arising.” He spoke forcefully about the way that white authorities, including the police, abused their power and brutalized Black people, describing a situation that was familiar to many people, but rarely spoken about in public.

“Malcolm’s irrepressible charisma and his debating skills made him a magnet for the media, and one of the most sought-after speakers on college campuses across the country,” the Paynes wrote.

The mainstream media — which was almost wholly white — treated Malcolm X as a “racist” and a dangerous agitator and referred to the Nation of Islam as a “cult.” But Malcolm X was also a person of intense fascination, a fiery and persuasive speaker who was voicing opinions that many Americans had never heard before.

His willingness to publicly criticize Martin Luther King Jr. — he would refer mockingly to the 1963 March on Washington as a “farce” — created a contrast between the two men that was seized upon by the press, and noted with interest by Malcolm X himself. According to Mr. Payne, Malcolm X began to describe himself “as a Black alternative that made King more acceptable to the establishment.”

In 1964, the year before his assassination, Malcolm X’s profile was further elevated. He visited the boxer Cassius Clay before Clay’s bout with Sonny Liston in February. After the fight, Clay defended the views Malcolm X; soon, he would change his name to Muhammad Ali. By then, Malcolm X had already parted ways with the Nation of Islam, in part because his fame made Mr. Muhammad envious.

That year, Malcolm X met Martin Luther King Jr. for the first and only time, gave a speech in favor of voter registration in which he used the memorable line “it’s ballots — or bullets” and embarked on another tour of African countries. Breaking with the Nation of Islam finally gave him license to campaign for civil rights, and he threw himself into the effort.

The following year, in February, he was assassinated.

Malcolm X was killed more than a half-century ago, but his influence is still very much alive in contemporary books, songs, films and in the national conversation about race.

A new book about his life, “The Dead are Rising: The Life of Malcolm X,” by Les Payne, was awarded this year’s Pulitzer Prize for biography. It was released last year, just months after the publication of another serious look at the political leader’s life: Peniel E. Joseph’s “The Sword and the Shield: The Revolutionary Lives of Malcolm X and Martin Luther King Jr.”

Even before those books refocused attention on his complicated legacy, the causes to which Malcolm X dedicated his life — racial justice, Black self-empowerment — were at the center of a vociferous protest movement that swept the country after the murder of George Floyd.

As the protests erupted, Malcolm X’s comments about Black pride and the importance of self-defense reverberated anew, just as they had during the police killings of Eric Garner, Michael Brown, and Tamir Rice in 2014.

Malcolm X’s place in popular culture has only risen in recent years, including in books, movies and music — especially hip-hop. Beyoncé included a snippet of one of his 1962 speeches in her 2016 song “Don’t Hurt Yourself.”: Malcolm X can be heard saying: “The most disrespected person in America is the Black woman.”

And Kanye West’s 2010 song “Power” includes the line “No one man should have all that power” — believed to be inspired by a police officer’s line in Spike Lee’s 1992 biopic, “Malcolm X.”

That film, released nearly 30 years after Malcolm X’s death, brought the political leader back to life for many. The film depicts his entire life, covering his early years committing crimes, his formative time in prison when he discovered the Nation of Islam, and his later years as a Black leader, including his assassination.

A more recent television project may even have played a role in the decision to reinvestigate his murder. The Manhattan district attorney’s office announced in early 2020 that it would review the case the same month that Netflix began streaming a six-part documentary, “Who Killed Malcolm X?”

And many figures in popular culture have for years clamored for answers to that question, including Chuck D. of Public Enemy, a hip-hop group. Most experts on the assassination long ago concluded the authorities had arrested and convicted the wrong men. They have also raised questions about whether the F.B.I. and the New York Police Department did all they could to avert the assassination.

“Whenever the government gets involved in anything, it’s going to be messy,” Chuck D. said on Wednesday after it became public that two of the men convicted of killing Malcolm X were set to be exonerated. “Once you bomb a place, it’s hard to all of a sudden clean up the room.”

For decades, the killing of Malcolm X has captivated the attention of scholars with a critical question: Were the wrong men convicted of the crime?

One of three men, Mujahid Abdul Halim, confessed at the 1966 murder trial. But he also testified that his co-defendants — Muhammad A. Aziz and Khalil Islam — were innocent and that he knew, but would not name, the actual assassins.

A decade later, Mr. Halim gave two sworn affidavits as part of an unsuccessful appeal by Mr. Aziz and Mr. Islam. In the documents, he named four other men who he said took part in the assassination, all members of a Nation of Islam mosque in Newark. He gave only partial names.

The review by the Manhattan district attorney’s office did not pin the crime on any other suspects. But scholars have formed their own conclusions about the identities and roles of the four men identified by Mr. Halim, who previously went by the name Talmadge Hayer.

It is widely believed among experts on the assassination that William Bradley, a member of the Newark mosque who once served time in prison on charges that included threatening to kill three people, fired the first shotgun blast. Mr. Halim identified the man with the shotgun as William X. Mr. Bradley denied any involvement and died in 2018.

The historian Manning Marable, who wrote a Pulitzer Prize-winning biography of Malcolm X in 2011, suspected that Mr. Bradley was probably pulled into the assassination plot by two other members of the Newark mosque whom Mr. Halim identified: Leon Davis and Benjamin Thomas.

Mr. Marable theorized that Mr. Davis and Mr. Thomas were most likely directed by a minister at the mosque to plan the assassination after Malcolm X returned to the United States from a trip abroad in 1964 and eventually enlisted the other men.

Most historians have concluded that Mr. Davis was seated with Mr. Halim in the first row of the ballroom, and they began firing handguns at the leader after the shotgun blast hit him.

At the time, Mr. Davis was about 20, lived in Paterson, N.J., and worked at an electronics plant. His name appears in a previously undisclosed 1965 F.B.I. report that says a New York police lieutenant was looking for him, the district attorney’s investigators said. It is unclear what that search yielded.

Mr. Thomas, who died in 1986, was 29 and an assistant secretary at the Newark mosque at the time of the assassination. It was at his home on the day before the killing, Mr. Marable wrote, that the team members ironed out details of the plot, including that Mr. Bradley would fire the first round.

Historians like Baba Zak Kondo believe that the fifth man involved was Wilbur McKinley, a 30-year-old construction worker at the time who is probably now dead. In an affidavit, Mr. Halim said a man named “Wilbur” or “Kinly” had created a diversion at the back of the ballroom before the shooting, igniting a furled sock as a makeshift smoke bomb.

Still, historians emphasize that other details of the plot are as significant as the men who they believe were directly responsible for carrying it out. It remains a matter of debate who ordered and planned the killing.

“The question is not simply the other four men who did kill Malcolm,” David Garrow, a Pulitzer Prize-winning civil rights historian, says in the second part of the Netflix series. “The more historically crucial questions are who else in Newark, in New York and most essentially, in Chicago, were active participants in arranging Malcolm’s murder.”

Since the assassination of Malcolm X in 1965, uncertainties have plagued historians and scholars, and questions about key details of the case have lingered. Here is a timeline:

Feb. 21, 1965

Malcolm X is assassinated in Upper Manhattan.

Malcolm X was killed as he addressed a crowd of roughly 400 people at the Audubon Ballroom at Broadway and 165th Street in Washington Heights. He was pronounced dead later that day.

March. 10, 1965

3 Nation of Islam members are indicted in the killing.

Mujahid Abdul Halim, a member of the Nation of Islam, was arrested as he fled the ballroom. (He was known as Talmadge Hayer at the time and later as Thomas Hagan.)

Within two weeks, two other men were arrested and later indicted in the killing: Muhammad Abdul Aziz (formerly Norman 3X Butler) and Khalil Islam (also known as Thomas 15X Johnson).

Feb. 28, 1966

Mujahid Abdul Halim confesses and says the other two men are innocent.

The trial over Malcolm X’s killing began on Jan. 22, and all three men took the witness stand to deny the accusations. But several weeks later, Mr. Halim testified a second time, telling jurors that he had been involved in the murder and that his two co-defendants were innocent. He declined to name the real killers.

Still, the jury convicted all three men, and they were later sentenced to 20 years to life in prison.

1977 to 1978

Mujahid Abdul Halim files two affidavits implicating four other people in the murder.

Mr. Halim filed two affidavits between 1977 and 1978 that detailed the logistics of the killing and reasserted his claim that his two co-defendants were innocent. He gave partial names of four members of a Nation of Islam mosque in Newark, N.J., saying they had been his partners in the assassination.

A defense lawyer moved for the case to be reopened in light of new evidence, but a judge denied the motion.

1985 and 1987

Muhammad Abdul Aziz and Khalil Islam are granted parole two years apart.

After Mr. Aziz’s attempts to be released on parole had been twice denied, his application was approved in 1985, and he was released after 20 years in prison, when he was 46 years old.

Two years later, Mr. Islam was also granted parole. He died in 2009.

Mr. Halim was released in 2010.

2011

The Justice Department declines to reinvestigate the case.

The publication of Manning Marable’s “Malcolm X: A Life of Reinvention,” a best-selling biography that attempted to reshape the perception of Malcolm X’s legacy, spurred new calls for the Justice Department and the New York State attorney general to start full investigations into the assassination.

Experts argued that a review could be conducted under a federal law that allows cold cases of violent crimes against Black people that predate 1970 to be reopened. But the calls for a new investigation went nowhere.

February 2020

The Manhattan D.A. says he will review the case as a Netflix series airs.

The Manhattan district attorney, Cyrus R. Vance Jr., announced that he was beginning a preliminary review of the case as Netflix released a series that argued that Mr. Aziz and Mr. Islam could not have been at the Audubon Ballroom when Malcolm X was killed.

“Who Killed Malcolm X?” explored the potential culpability of the four members of the Nation of Islam mosque in New Jersey mentioned in Mr. Halim’s affidavits. The episodes depicted the four men’s involvement as an open secret in the city.