From the moment that 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 affront, a betrayal — an egregious breach of trust among 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 U.S. 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 familiar with the matter.

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

In the past, U.S. authorities worked with their Mexican counterparts in capturing major drug trafficking suspects, with the Mexicans often making the arrests, but not in this case; the Justice Department quietly indicted Cienfuegos last year, and then waited until he visited the United States to take him into custody. To forgo Mexican cooperation, anger an important ally and then retreat from prosecution is a serious setback for the department.

The story of Cienfuegos, who will soon head home to Mexico to face an uncertain future, is in a sense a cautionary tale about the effects of international politics on the day-to-day prosecution of the drug war. In a letter to the Brooklyn federal judge, Carol B. Amon, prosecutors said they had dropped the charges because of “sensitive and important foreign policy considerations.”

At a hearing in New York on Wednesday morning, Seth DuCharme, a former top aide to Barr who now serves as the acting U.S. attorney in Brooklyn, elaborated somewhat on those considerations, saying that by releasing Cienfuegos he was seeking to protect “the United States’ relationship with Mexico,” particularly where joint law enforcement matters were concerned.

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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 United States for “listening to our position and rectifying.”

The U.S. ambassador had informed the Mexican foreign minister of Cienfuegos’ arrest soon after he was apprehended at the Los Angeles airport, sparking an uproar inside 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 Cienfuegos should have been spared prosecution, but that U.S. 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.

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

When asked how to interpret the lack of communication from U.S. officials, López Obrador did not mince 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,” he said.

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, Ebrard said in an interview with Proceso magazine. “There will be cooperation, but it will have to be on a different basis. Everything should be different.”

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.

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The charges were the result of a multiyear inquiry that investigators called Operation Padrino, or Godfather — a reference to what they claim was 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 Cienfuegos in chatting and orchestrating meetings with cartel leaders.

Officials say that 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, Cienfuegos also directed military operations away from the cartel and toward its rivals.

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

One of the people familiar with the matter said that the prosecutors who had built the case against Cienfuegos were “devastated” that their superiors had decided to drop the pursuit of him in U.S. courts. Though Barr suggested in a news release Tuesday that 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, 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.

Sapone added that he had been prepared to challenge 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 Amon with a motion to dismiss the charges.

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