After the students were kidnapped from Iguala, the search for the disappeared turned up 28 other bodies in nearby mass graves. They had been killed and buried in apparently separate circumstances. An October 2014 internal report from the U.S. Army’s Northern Command noted the extra bodies, and said that the preponderance of mass graves raised “alarming questions about the widespread nature of cartel violence in the region and the level of government complicity.”

New evidence provides a rare glimpse of the way U.S. authorities have learned that the Mexican security apparatus has been implicated in specific abuses, and how they have responded.

U.S. government documents obtained by the National Security Archive through Freedom of Information Act requests demonstrate that the United States is well aware that its support is going to Mexican authorities connected to abuses. And yet, with few exceptions, the money keeps flowing.

In this context, U.S. cooperation with the Mexican government — which entails billions in American financial backing for its war on drugs — is receiving renewed scrutiny.

In the span of less than a year, these three incidents have implicated local, federal, and military authorities, providing graphic examples of the state-sponsored violence that has become so prevalent in Mexico.

Iguala, however, was just one among many recent atrocities in Mexico. The previous June, Mexican soldiers killed 22 people in Tlatlaya, in the state of Mexico. Then last month, Mexican journalists reported that federal police had massacred 16 people in January in Apatzingán, in the western state of Michoacán. In each case, authorities allegedly tried to cover up the killings.

The case of 43 missing students from Ayotzinapa teachers college, who were kidnapped last September from the Mexican city of Iguala and have not been seen since, has caused an international outcry and rocked the presidency of Enrique Peña Nieto. The Mexican government has sought to portray the Iguala case as the work of local government officials and their gangster accomplices, but as The Intercept reported this week , evidence implicating authorities in the disappearances has led to a concentration of popular anger in a single phrase: fue el estado. “It was the state.”

The Northern Command report also highlighted the case of Tlatlaya. Some of the 22 killed there, who the government alleged were cartel members, died during a firefight, while others had been summarily executed afterwards. A Mexican army officer and seven soldiers had recently been arrested for the killings and subsequent cover up, and Northern Command “assesse[d] that as more facts come to light there is greater acceptance that the military was involved in wrongdoing.”

The commander of the military zone overseeing the battalion responsible for the Tlatlaya killings was also put under investigation by the Mexican military. If he were to be implicated in “a gross human rights violation,” the report notes, “the entire military zone and 10,000 personnel will be ineligible for U.S. security cooperation assistance.”

Soon enough, at least the battalion directly involved was cut off: In January, another Northern Command cable reported that the State Department “has suspended U.S. funded assistance to this unit pending the results of this investigation.”

A State Department official confirmed to The Intercept that five individuals in the unit had received training from Northern Command, but that none of those specific trainees had been charged in the killings. Beyond that, she said, “the U.S. government has not provided any assistance or trained members of the 102nd battalion and will not do so until it has evaluated the results of the investigations related to this incident.”

Legislation introduced by Senator Patrick Leahy, D-Vt., in 1997, and commonly known as the “Leahy Law,” prohibits U.S. assistance to foreign security forces credibly believed to have committed a gross human right violation.

The Tlatlaya incident is a rare confirmed example of the U.S. government actually cutting off funding for security forces.

In the case of the missing Ayotzinapa students, when asked if the State Department or Department of Defense has suspended any training or assistance to security forces or investigative agencies in the state of Guerrero, where the students disappeared, the official said that the State Department has not received any requests for funding from the Mexican government to train security forces or investigative agencies in Guerrero since last fall. She did not confirm, however, if any units or agencies had actually been suspended as a result of the investigations stemming from the disappearance. The Department of Defense did not respond to requests for comment.

The State Department’s piecemeal response to these events highlights the conundrum that Mexico now presents for the United States, as it seeks to help the Mexican government battle drug cartels.

Since 2008, the U.S. government has spent nearly $3 billion on security aid to Mexico, largely through the Mérida Initiative, a counter-drug strategy modeled on Plan Colombia, through which the United States funneled billions of dollars to that country’s often-brutal drug war. This support comes in addition to direct sales of arms and other equipment, which totaled over $1.15 billion last year alone. Mexico recently surpassed Colombia to become the largest customer for U.S. weapons in Latin America.

Documents revealing details of this cooperation show how U.S.-Mexico security and intelligence relations have reached unparalleled levels of intimacy. In 2010, with the Mérida initiative in full swing, the U.S. Embassy noted in a cable released by Wikileaks that “our ties with the Military have never been closer in terms of not only equipment transfers and training,” but also “intelligence exchanges.”

In recent years, the Obama administration has shifted the emphasis of Mérida funds from military hardware to programs focused on institutional reform, including training law enforcement at the local level. But the Mexican government’s disastrous record on investigating and punishing the perpetrators of recent crimes raises the question of what good that assistance is doing.

A Mexican government database lists over 23,600 people who have been reported disappeared throughout the country; 2014 witnessed 5,133 disappearances, the highest number on record. Impunity remains the norm, with 98.3 percent of crimes going unpunished in 2013, according to Mexican government statistics. The U.S. State Department’s own human rights reporting on Mexico highlights police and military involvement in serious abuses, including unlawful killings, physical abuse, torture and disappearances.

“Clearly elements within the [Mexican] Army believed that they had nothing to fear by slaughtering innocent people execution-style, which indicates a pervasiveness of impunity,” said Tim Rieser, foreign policy aide to Senator Leahy, who has been a longtime advocate for greater pressure on Mexico on human rights, in reference to the Tlatlaya case. “So clearly there’s a long way to go.”

The Mexican government’s failure to investigate mass graves provides a revealing example of the problem of impunity.

Hundreds of mass graves have been discovered in Mexico in recent years. Despite that, Mexico’s federal prosecutors have reported opening just 15 investigations between 2011 and April 2015, according to documents obtained by the human rights organization Article 19.

This is clearly an inadequate response to the scale of the problem, of which U.S. officials in Mexico are acutely aware. One U.S. Embassy cable from 2011 reported on the discovery of 219 bodies unearthed in a series of mass graves that year around the northern city of Durango. Another cable, from 2010, discusses a mass grave in Acapulco, Guerrero containing the bodies of 18 men, and another near a ranch in the northern state of Chihuahua, filled with 19 men and one woman.

As these graves and others like them apparently go uninvestigated, the U.S. has been pouring money into Mexico’s investigative and forensic capabilities. The same document that reports on the mass graves in Acapulco and Chihuahua discusses U.S. deliveries of approximately $1.2 million in equipment to a laboratory that provides training for the attorney general’s forensic experts. The document also highlights plans to provide the Mexican government with network, forensic, and biometric equipment, beginning in July 2011.

An upbeat Embassy memo from January 2013, “summarizing the achievements” of Mérida, reports that the U.S. Justice Department had received over $11 million under Mérida to spend on forensics development and planned to expand its support to state-level laboratories that year.

Despite this aid, the Mexican government has fallen so woefully short that family members of Mexico’s disappeared have found it necessary to take up the task of investigation on their own. Since her brother was kidnapped and disappeared by armed men in police uniforms in October 2013, Nansi Cisneros has dug into the case herself, and started an organization to help other families do the same.

“The state or the government is not giving us answers,” Cisneros told The Intercept. “It’s become up to us to try to find our loved ones.”

The U.S. government has also known about cases where the Mexican government has opened investigations into mass graves only to suppress them later. As the National Security Archive has documented, in 2011, when mass graves were discovered in Northeastern Mexico containing the remains of victims of the Zetas cartel, U.S. officials knew that Mexican authorities were downplaying the massacres and removing remains to make the body count appear less alarming, jeopardizing investigations in the process. (Mexican authorities later released files implicating local police in the crime.)

The United States is not just sending after-the-fact assistance for crime scenes. Declassified government files from U.S. and Mexican agencies also show how Washington has exported intelligence-gathering technology to Mexico’s army, federal, state and local police forces, and prosecutors.

A host of U.S. agencies have supported Mexican wiretap capabilities, according to a White House counternarcotics strategy document from 2010, and biometric technology, per a 2011 Embassy cable. The FBI has also provided assistance in fingerprint collection, Mexican government files show. The State Department’s 2013 summary of Mérida achievements notes that “the U.S. provides training to officers in twenty-one different states,” including supplies from “gym equipment to training handcuffs,” and training in “specialized intelligence analysis.” At the federal level, the cable notes, the U.S. has trained specialty areas including “explosive devices, terrorism, and drug trafficking.”

As of December 2012, the memo reports, the State Department had funded nearly $4 million in “basic undercover surveillance equipment,” along with training for Mexican federal investigative agencies.

The State Department has deployed contractors to provide software, equipment and other assistance for Mexico’s National Command and Control Center, known as the “Bunker,” which is used by the federal police as an information-gathering and intelligence-sharing hub. Mexico’s security agencies are also connected through a network called Plataforma México — another U.S.-funded project that links the national Bunker to other federal, state and local agencies including regional Command and Control Centers, known as C-4s. The more sophisticated C-4s in Mexico’s northern region communicate directly with U.S. agencies, such as Department of Homeland Security offices across the border.

The effectiveness of all this intelligence gathering and information sharing equipment against criminal activity is questionable. U.S. consular officials in Monterrey, in a 2009 assessment released by Wikileaks, wrote that “neither Plataforma México” nor the local C-4 “have hindered cartel operations.”

C-4s certainly didn’t help in the case of the forty-three missing Ayotzinapa students. As The Intercept detailed, internal records produced by Guerrero state investigators show that the regional C-4s near the site of the students’ kidnapping transmitted information on the movement of the students the night that they were attacked. But neither federal law enforcement nor the military intervened to stop the violence.

While the State Department condemned the “horrific events” in Iguala, the U.S. remains publicly supportive of Peña Nieto. Obama has called him a “friend and partner” and defended security assistance in recent months.

The Intercept asked the State Department for a list of all Mexican units that have been cut off from U.S. funding because of human rights violations since the Mérida initiative began, but the spokesperson said it was not yet publicly available.

“It’s incomprehensible that they don’t already have that list,” said Laura Carlsen, Mexico City-based director of the Americas Program, in an email to The Intercept. Carlsen has worked for years with a coalition of human rights groups to bring attention to the consequences of U.S. support for the drug war in Mexico.

“The bigger picture is that this aid does go to human rights violators. U.S. taxpayer dollars are supporting a drug war that emboldens abusive government forces that are executing and disappearing Mexican citizens. No amount of withholding or [human rights] conditioning will change that,” Carlsen said.

In February of this year, Obama asked Congress for an additional $80 million for Mérida programs, on top of $300 million already approved by Congress last year. More funding for judicial reforms and forensics were also approved last year.

Family members of Mexico’s missing have been trying to draw attention to the connection between U.S. aid and violence and impunity in Mexico.

Nansi Cisneros, the woman whose brother was kidnapped in 2013, joined advocacy groups in Washington, D.C. last week to call for an end to security aid to Mexico. She delivered a letter to Senator Marco Rubio, R-Fl., on behalf of family members of the disappeared, asking for greater scrutiny on “the human rights catastrophe right next door in Mexico,” and urging him to “hold a hearing on human rights violations, specifically enforced disappearances, in Mexico committed by the Mexican state.”

Felipe de la Cruz Sandoval, a professor at the Ayotzinapa teachers college whose son survived the attack last September, was part of a caravan of students’ family members who traveled to the U.S. this spring.

“If President Obama has human thoughts and feels the pain of the Mexican people, he should be reviewing the political relations and the agreements with Mexico,” Sandoval said in a press conference outside the Mexican consulate in New York. “He should consider if a life is more important than a political and economic agreement on weapons with Mexico, because these weapons are being used to kill students in Mexico.”

Several of the documents cited in this article were obtained through Freedom of Information Act requests filed by researchers with the National Security Archive. Visit the Migration Declassified project site for more, and for access to more of the document collection on U.S. foreign policy and human rights in Mexico, see Mike Evans’s briefing book publication, “Mexico: Los Zetas Drug Cartel Linked San Fernando Police to Migrant Massacres.” See also Mike Evans and Jesse Franzblau’s “Mexico’s San Fernando Massacres: A Declassified History.”

Photo: Gregory Bull/AP