This article was originally published at Propublica. ProPublica is a Pulitzer Prize-winning investigative newsroom. Sign up for The Big Story newsletter to receive stories like this one in your inbox.

On Oct. 15, 2020, federal prosecutors took the remarkable step of arresting former Mexican Defense Minister Gen. Salvador Cienfuegos Zepeda on charges that he conspired to protect drug traffickers. Even in retirement, Cienfuegos was the most important Mexican official ever charged in a U.S. court. A month later, however, the Justice Department took the even more extraordinary step of dropping the charges.

The U.S. attorney general, William P. Barr, said his chief goal in sending Cienfuegos home was to preserve Mexico’s collaboration with the United States in fighting the drug trade. But the general’s arrest and its aftermath had the opposite effect — all but shutting down counterdrug cooperation between the two countries. Less than two months after his return, Mexican prosecutors exonerated Cienfuegos after a cursory investigation, underscoring the impunity with which the military has operated in the drug fight. President Andrés Manuel López Obrador then began attacking the Drug Enforcement Administration for “fabricating” its charges against Cienfuegos.

Last year, Mexico abandoned the Mérida Initiative, the 2007 landmark agreement by which the United States provided Mexico with more than $3.5 billion in aid and training to fight organized crime. The new pact that replaced Mérida is very much on López Obrador’s terms. Joint operations against big traffickers have been almost an afterthought. Meanwhile, fentanyl from Mexico is fueling the deadliest drug epidemic in U.S. history.

U.S. investigators believed that with Cienfuegos’ arrest they had finally confronted the high-level corruption that has long sustained organized crime in Mexico. Instead, they now say, the episode is likely to define the limits of U.S. security policy in Mexico for years to come.

The Cienfuegos case emerged from a routine DEA investigation in Las Vegas and a code word: “godfather.”

The agent who drove the investigation was a Las Vegas police detective named Timothy Beck. He spoke almost no Spanish and had never worked in Mexico. But he and other agents built a powerful case against the leaders of a violent drug gang, called “the H’s,” who were based in the small Pacific Coast state of Nayarit.

Using court-authorized wiretaps in the United States, the Las Vegas task force collected years of the gang’s communications. The U.S. agents followed its leader, Juan Francisco Patrón Sánchez, known as H-2, as he worked closely with corrupt officials in Nayarit. The agents watched as H-2 and his lieutenants then sought protection from higher-level officials in Mexico City — one of whom they called their “godfather.” The agents later concluded that the official was Cienfuegos.

(Cienfuegos could not be reached for comment, but in a statement, his lawyer said: “General Cienfuegos never should have been charged. And no dismissed indictment or newspaper story will ever change that. The fact is, General Cienfuegos remains as American jurisprudence presumes him: innocent.”)

A key source in the investigation set off a firestorm within the U.S. government.

In early 2017, H-2 and his lieutenant were killed along with a dozen of their gunmen by a special-operations team of Mexican marines. That unit, led by Adm. Marco Antonio Ortega Siu, had worked closely with the DEA and other U.S. agencies for years. But U.S. officials had no warning that the marine team was going after the H’s.

(Ortega Siu, who is now retired, could not be reached for comment. A spokesperson for the Mexican navy declined to answer questions about the marines’ actions in Nayarit, saying that such operations needed to remain confidential for reasons of national security.)

Not long after the H’s were killed, Nayarit’s acting attorney general, Edgar Veytia, was arrested crossing into the United States. He told investigators a shocking story about what he said really happened in the marines’ raid.

Senior Justice Department officials turned confidentially to the Mexican attorney general’s office to investigate the matter. However U.S. officials said the Mexicans appeared to do nothing. The DEA aggressively sought to discredit Veytia, whom they saw as jeopardizing their most important partners in Mexico. However, Justice Department officials said that many of his claims appeared to be true.

The Cienfuegos indictment was part of a broader U.S. effort to take on high-level drug corruption in Mexico.

Behind the general’s indictment in the Eastern District of New York was a new, joint push by DEA agents and prosecutors to take on the high-level corruption that U.S. officials believe has long sustained Mexico’s drug trade. The prosecutors were reacting in large part to embarrassing testimony in the 2018 trial of Mexican drug boss Joaquín Guzmán Loera, known as El Chapo, from witnesses who said he paid huge bribes to top Mexican officials with whom the United States had worked closely.

For their part, DEA officials in Mexico were frustrated with constraints imposed on them by the new López Obrador government. After connecting with the Eastern District prosecutors, a team of experienced agents began to dig into the evidence they had on government figures who had protected drug gangs. The effort, which has not been previously reported, eventually identified more than 20 targets for prosecution among current and former Mexican officials.

Returning Cienfuegos to Mexico was William Barr’s call.

After Cienfuegos’ arrest, Mexico’s foreign minister, Marcelo Ebrard, complained angrily to U.S. officials that they had betrayed Mexico’s trust. Ebrard warned that counterdrug cooperation and even the DEA’s presence in Mexico could be at stake. According to several officials, Barr decided on his own to drop the most significant Mexican corruption case that U.S. prosecutors had ever brought.

The attorney general later said he hadn’t been properly informed about Cienfuegos’ arrest, but current and former Justice Department officials disputed that assertion. They said Barr was briefed at least three times before the general’s arrest. Barr did have doubts about the strength of the evidence against Cienfuegos, department officials said. But he gave the Eastern District prosecutors little opportunity to defend their case, which officials said included some new witnesses who could testify about the gang’s relationship with Cienfuegos and other traffickers who said they met with the general directly. (Through a spokesman, Barr declined to comment on his involvement in the Cienfuegos case.)

Barr did not consult President Donald Trump or senior staff from other national security agencies about his decision, officials said. Nor did he set any conditions for the general’s return, U.S. and Mexican officials said. Instead, Barr emphasized Washington’s interest in a fugitive Mexican drug trafficker, Rafael Caro Quintero, who had been convicted of murdering a DEA agent in 1985. Caro Quintero was arrested earlier this year. Barr also asked the Mexican government to protect confidential evidence that U.S. officials shared in the Cienfuegos case. Instead, López Obrador released the information publicly and later dismissed it as “garbage.”

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