MEXICO CITY — The Mexican president said his government had finally solved the mystery behind the haunting disappearance of 43 students, one of the worst human rights abuses in the country’s recent history.
In August, the government unveiled a truth commission report saying that after being abducted in 2014, the students were killed by drug traffickers working with the police and the military. A slew of arrest warrants followed.
But since then, the case has unraveled. Arrest warrants for military suspects were revoked. The lead prosecutor resigned. And now, the backbone of the government’s explosive new report is in question.
In an interview with The New York Times, the head of the truth commission said that much of what it presented as crucial new evidence could not be verified as real.
“There’s a percentage, a very important percentage, that is invalidated,” said the official, Alejandro Encinas.
The extraordinary admission — along with a review of government documents, a previously undisclosed recording and interviews with several people involved in the inquiry — points to how the government’s rush to deliver answers resulted in a series of missteps: a truth commission that relied on unsubstantiated evidence and a criminal investigation that botched the prosecution of key suspects.
Pressure came from the very top: Mexico’s president, Andrés Manuel López Obrador, announced in June that his government knew what happened to the missing students and would put the matter to rest this year, even though investigators hadn’t yet nailed down the proof.
But problems also stemmed from dysfunction within his administration, where officials investigating the abduction withheld key information from one another, undermining their own case.
Instead of a political victory, a campaign promise to finally close an open wound in the country has become a liability for the president, as families of the missing students have slammed the government for failing to deliver truth or justice.
“They needed to do something impeccable, but they didn’t,” said Santiago Aguirre, the primary lawyer representing the families. “It ends up looking a lot like what happened before, finishing up without verifying, more out of politics than out of conviction of having the truth clarified.”
On the night they vanished in September 2014, the students, in keeping with a tradition that was largely tolerated by local bus companies, had commandeered a number of buses to drive to a demonstration in Mexico City commemorating a 1968 student massacre.
But the students were intercepted by gunmen, including municipal police officers, who forced them off the buses, shot some of them and took the rest away. After that, little is known about what happened.
The government of President Enrique Peña Nieto fumbled its investigation, producing a version of events it called “the historical truth” that blamed drug traffickers and local police officers, and was disputed by international investigators. Even as evidence emerged linking federal security forces to the abduction, most of the students were never found.
For Mr. López Obrador, the case carried special significance.
The victims — students at a rural teachers college in Ayotzinapa, a poor community in southern Mexico — were at the core of his base of support. The deeply flawed investigation under Mr. Peña Nieto fed a broader wave of discontent with the political establishment in Mexico, which favored the outsider candidacy of Mr. López Obrador and helped sweep him into power in 2018.
As president, Mr. López Obrador’s first executive order created a truth commission to investigate the disappearance. To lead the inquiry, he appointed Mr. Encinas, a longtime friend and former senator.
Families of the students were brought to the national palace for regular meetings, and felt that finally they were being taken seriously. The government opened a separate criminal investigation, helmed by a widely respected special prosecutor, Omar Gómez Trejo. The remains of two students were identified.
But after three years passed without much else in the way of groundbreaking developments, Mr. López Obrador began to grow anxious.
“The president asked me, ‘What happened? Release the information,’” Mr. Encinas said in an interview, later adding: “We have two years left in the government, we have to show results, and the attorney general’s office has to prosecute.”
So in February, Mr. Encinas scrambled for answers: He flew to Israel to meet alone with Tomás Zerón de Lucio, a former Mexican official accused of deliberately compromising the previous administration’s investigation into the abduction.
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Mr. Zerón, the former director of Mexico’s equivalent of the F.B.I. who now lives in Israel and is applying for asylum there, has been charged with torturing witnesses and planting evidence. In January, Mexico submitted to Israel an extradition request for Mr. Zerón.
A month later, during a nearly three-hour lunch in Tel Aviv, Mr. Encinas pleaded with Mr. Zerón for information about the students’ remains that he may have withheld while in power — offering the “president’s support” in exchange for his cooperation, according to a recording of the conversation reviewed by The Times.
“Help me unravel all of this,” Mr. Encinas told Mr. Zerón during the meeting. “I’m promising you the president’s support.”
Any doubts Mr. Zerón raised about beating his case were batted away.
“The president doesn’t care about putting anyone in jail,” Mr. Encinas told the former Mexican official, who faces up to 60 years in prison.
“To sit down with the man who has been identified as the mastermind in the cover-up of what happened, it seems like a desperate measure,” said Kate Doyle, a senior analyst at the National Security Archive, a Washington-based research institute, and an expert on the disappearance. “The government is obviously scrambling to gather whatever information it can to be able to say that it has solved the case.”
In an interview with The Times, Mr. Encinas said he was trying to persuade Mr. Zerón to cooperate because he believed he had valuable information and that he was only promising Mr. López Obrador’s support for a deal that could have included a reduced prison sentence.
Liora Turlevsky, Mr. Zerón’s lawyer said the meeting shows “that the accusations against my client are a serious blood libel and a witch hunt that was conducted due to internal political interests.” Mr. Zerón, she said, denies all accusations against him and is not withholding any information connected to the case.
A spokesman for the president did not respond to requests for comment.
The trip to Israel yielded no new information. But two months later, in April, Mr. Encinas finally got what seemed to be a big break: a trove of WhatsApp messages purportedly sent in 2014 by criminals, members of the military and other officials previously implicated in the abduction.
The messages appeared to lay out in gruesome detail how and where drug traffickers disposed of the students’ bodies, according to an unredacted copy of the government’s report reviewed by The Times.
The messages also suggested, for the first time according to experts in the case, that a senior military officer was directly involved in the disappearance of six of the students.
Then in June, Mr. López Obrador announced that the government had figured out what happened to the missing students. “The Ayotzinapa matter will be done this year,” Mr. López Obrador said.
In the weeks that followed, officials rushed to fulfill that promise, making decisions that directly undercut their own investigation — in part because people working side by side on the case did not fully trust one another.
The messages, shared with Mr. Encinas by a single source as a series of 467 screen captures, were cross referenced with other pieces of evidence. But Mr. Encinas did not share them with the attorney general’s office, even though, he said, those officials could have done a forensic analysis to verify the messages’ authenticity.
Mr. Encinas withheld the messages because he worried they would be leaked, he said, and he felt an obligation to present “a timely” report to the students’ families.
A similar sense of urgency had taken hold in the attorney general’s office.
As Mr. Encinas was getting ready to unveil his findings in August, the attorney general, Alejandro Gertz Manero, pushed his lead prosecutor to prepare an arrest warrant for the former attorney general, who became the face of the previous administration’s sham investigation, according to several people familiar with the matter who spoke on the condition of anonymity for fear of reprisals.
The lead prosecutor, Mr. Gómez Trejo, begged for more time to gather additional evidence against the former attorney general but was overruled, the people said. Prosecutors with little experience on the case then took it over, and the former attorney general was arrested.
But the case against him was later suspended by a judge who openly admonished the new prosecutors for shoddy work.
Then, weeks after angering leaders of the armed forces by requesting arrest warrants for military officers, prosecutors reversed course and asked a judge to cancel more than a dozen of them, citing, among other issues, “deficient evidence” in their own case. Mr. Gertz Manero’s office also launched an internal audit of the case compiled by Mr. Gómez Trejo, who resigned after being sidelined.
Four military officers, including a general, remain in custody and are awaiting trial.
The truth commission was also in trouble. Almost as soon as Mr. Encinas published his report, the WhatsApp messages became a focus of scrutiny. A team of international investigators who have been following the case for years pointed out that the messages’ tone differed from what they had seen in other intercepted communications.
After questions about the messages surfaced publicly, Mr. Encinas subjected them to a more thorough review. He said that he had been unable to verify many of the screenshots, and has had to scrap some of them.
“There are some we’ve had to discard,” he said. “They don’t have enough elements to be confirmed.” Mr. Encinas conceded that the source who provided the messages could have fabricated them. “Anything is possible,” he said, “There is no 100 percent guarantee.”
The international investigators are expected to publish their own analysis of the messages later this month. “We are doing that verification for the parents,” said Ángela Buitrago, one of the investigators.
Mr. Encinas said that even if the messages turned out to be fake, he still had confidence in his investigation, which he said was backed up by other evidence and was “solid and getting even stronger.”
“Every investigation,” Mr. Encinas said, “has its successes and its errors.”
Natalie Kitroeff and Oscar Lopez reported from Mexico City, and Ronen Bergman from Tel Aviv.