From the moment U.S. federal agents arrested a former Mexican defense minister last month on drug trafficking charges, the highest levels of the Mexican government were outraged at being kept in the dark about the case, seeing it as an egregious breach of trust between allies.

Those emotions reached a peak in recent days, as Mexico City issued an unheard-of warning to its counterparts in Washington: If the United States did not rethink its pursuit of Salvador Cienfuegos Zepeda, Mexico would consider expelling American federal drug agents from the country, jeopardizing a decades-long partnership that has helped bring several top drug lords to justice, according to three people in the United States who are very close to the case.

That threat appeared to work. On Wednesday, at the request of Attorney General William P. Barr himself, a federal judge in Brooklyn said she would formally dismiss the charges against Mr. Cienfuegos, a former army general.

The Justice Department’s reversal stunned officials in the State Department and in Congress, who said Mr. Cienfuegos’s release would be an abrupt departure from the Trump administration’s aggressive pursuit of organized crime and drugs from Mexico.

Seth DuCharme, a former top aide to Mr. Barr who now serves as the acting U.S. attorney in Brooklyn, sought to explain the move, saying that by releasing Mr. Cienfuegos he was seeking to protect “the United States’ relationship with Mexico,” particularly where joint law enforcement matters were concerned.

But that explanation did not satisfy Senator Bob Menendez, Democrat of New Jersey and chairman of the Foreign Relations Committee, who said both Mr. Barr and Secretary of State Mike Pompeo needed to explain what had gone wrong.

“There is no explanation for Attorney General Barr’s decision to abruptly drop drug trafficking charges against General Cienfuegos,” Mr. Menendez said in a statement. “Cooperation with the Mexican government is essential for upholding our national security, and those bilateral ties must be built on common respect for our own rule of law and due process.”

In the past, U.S. authorities worked with their Mexican counterparts in capturing major drug trafficking suspects, who are often arrested in Mexico, by Mexican forces. Mr. Barr visited Mexico City twice last winter to discuss with Mexican officials closer cooperation on gang violence, drug trafficking and immigration.

But in this case the Justice Department quietly indicted Mr. Cienfuegos last year, did not alert Mexican officials, and waited until he visited the United States to take him into custody. It is not clear what led the department to forgo Mexican cooperation, angering an important ally and leading to the embarrassing setback of dropping the case.

The release of Mr. Cienfuegos — who will soon head home to Mexico as a free man, with no guarantee that he will ever face charges — illustrates how foreign policy can interfere with the day-to-day prosecution of the drug war. Prosecutors acknowledged the challenges in a letter to the Judge Carol B. Amon, of Federal District Court in Brooklyn, saying they had dropped the charges because of “sensitive and important foreign policy considerations.”

Credit…Oliver Contreras for The New York Times

Judge Amon, in dismissing the indictment, appeared to agree that there was little else to do about the charges.

“Although these are very serious charges against a very significant figure, and the old adage ‘a bird in the hand’ comes to mind,” she said, “still I have no reason to doubt the sincerity of the government’s decision.”

Word of the dismissed indictment was hailed as a triumph by the government in Mexico, where President Andrés Manuel López Obrador thanked the U.S. for “listening to our position and rectifying.”

The U.S. ambassador had informed the Mexican foreign minister of Mr. Cienfuegos’ arrest soon after he was apprehended at the Los Angeles airport, sparking an uproar inside Mr. López Obrador’s nationalist administration.

In the days following the arrest, high ranking officials gathered for a flurry of meetings in which they expressed fury at having been blindsided by one of their closest allies and strategized how to respond, according to two people familiar with the matter. The feeling in the room was not that Mr. Cienfuegos should have been spared prosecution, but that American law enforcement had violated their trust by keeping Mexico unaware of the investigation of such an important figure, the people said.

The military, one of the most powerful institutions in the country and a close ally of the president’s, was particularly livid at what was viewed as a violation of Mexican sovereignty. Enraged military officials pushed the government to take action.

The frustration quickly began to spill out into the public sphere.

When asked how to interpret the lack of communication from U.S. officials, Mr. López Obrador did not mince his words. “What’s not fair is that they operate in Mexico, they even link up with Mexican institutions, they extract information and reach a resolution without informing the Mexican government what it is they’re investigating.”

Marcelo Ebrard, Mexico’s foreign minister, suggested that the Cienfuegos capture had jeopardized the country’s extensive security cooperation with the United States. “There will be a revision” of Mexico’s collaboration with the U.S. Drug Enforcement Administration, Mr. Ebrard said in an interview with Proceso magazine.

“There will be cooperation, but it will have to be on a different basis,” he added. “Everything should be different.”

Credit…Marco Ugarte/Associated Press

Mr. Cienfuegos, who had served as Mexico’s defense minister from 2012 to 2018, was charged in Brooklyn in October with laundering money and trafficking heroin, cocaine, methamphetamines and marijuana from late 2015 through early 2017 on behalf of the H-2 drug cartel, an offshoot of a larger and older criminal mafia, the Beltrán-Leyva organization.

The charges were the result of a multiyear inquiry that investigators called Operation Padrino, or Godfather — a reference to what they claim was Mr. Cienfuegos’ nickname in the underworld. The investigation, which began in late 2013, was bolstered, court papers say, by a sprawling wiretap that covertly captured thousands of BlackBerry messages, some of which are said to implicate Mr. Cienfuegos in chatting and orchestrating meetings with cartel leaders.

Officials say that Mr. Cienfuegos helped the H-2 cartel, which has committed horrific acts of violence as part of its smuggling business, with its maritime shipments. In exchange for lucrative payouts, the officials say, Mr. Cienfuegos also directed military operations away from the cartel and toward its rivals.

At the court hearing on Wednesday, Mr. DuCharme said his office remained confident in the strength of its investigation and “stands behind the case.” But under questioning by Judge Amon, he admitted that the decision to drop the charges against Mr. Cienfuegos had been made “at the highest level of the Justice Department,” identifying Mr. Barr by name.

One of the people familiar with the matter said that the prosecutors who had built the case against Mr. Cienfuegos were “devastated” that their superiors had decided to drop the pursuit of him in U.S. courts. Though Mr. Barr suggested in a news release on Tuesday that Mr. Cienfuegos would be “investigated and, if appropriate, charged” in Mexico, it remained unclear what would happen once he was repatriated, which could happen as early as Wednesday evening.

Edward Sapone, Mr. Cienfuegos’ lawyer, said that he and partners had believed from the start of the case that their client’s arrest was unjust because it violated a treaty under which the U.S. government had agreed to notify the Mexican government in advance about the arrest of any high-level suspect.

Mr. Sapone added that he had been prepared to challenge Mr. Cienfuegos’ arrest — in motions or at trial if necessary — but that late last week, federal prosecutors reached out to him to let him know they were considering approaching Judge Amon with a motion to dismiss the charges.

“I commend to the U.S. attorney’s office for making litigation unnecessary,” he said.

Alan Feuer reported from New York, and Natalie Kitroeff from Mexico City. Oscar Lopez contributed reporting from Mexico City, and Katie Benner and Lara Jakes from Washington.

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