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MEXICO CITY — For the past seven years, Mexico and the United States have forged an unparalleled alliance against Mexico’s drug cartels, one based on sharing sensitive intelligence, U.S. training and joint operational planning.

But much of that hard-earned cooperation may be in jeopardy.

President Obama heads off Thursday on a three-day visit to Mexico to cement relations with the newly elected president, Enrique Peña Nieto, with vows of neighborly kinship and future cooperation.

Obama’s visit comes as the fight over border security and immigration overhaul has begun to consume Congress.

The December inauguration of Peña Nieto brought the nationalistic Institutional Revolutionary Party (PRI) back to power after 13 years, and with it a whiff of resentment over the deep U.S. involvement in Mexico’s fight against narco-traffickers.

The new administration has shifted priorities away from the U.S.-backed strategy of arresting kingpins, which sparked an unprecedented level of violence among the cartels, and toward an emphasis on prevention and keeping Mexico’s streets safe and calm, Mexican authorities said.

Some U.S. officials fear the coming of an unofficial truce with cartel leaders. The Mexicans see it otherwise. “The objective of fighting organized crime is not in conflict with achieving peace,” said Eduardo Medina-Mora, Mexico’s ambassador to the United States.

Two weeks after Peña Nieto assumed office Dec. 1, the new president sent his top five security officials to an unusual meeting at the U.S. Embassy in Mexico City. The new attorney general and interior minister sat in silence next to the new leaders of the army, navy and Mexican intelligence agency.

Also at the Dec. 15 meeting were representatives from the U.S. Drug Enforcement Administration (DEA), the CIA, the FBI, the Office of the Director of National Intelligence and other U.S. agencies charged with helping Mexico destroy the drug cartels that had besieged the country for the past decade.

The Mexicans remained stone-faced as they learned how entwined the two countries had become during the battle against narco-traffickers, and how, in the process, the United States had been given near-complete access to Mexico’s territory and the secrets of its citizens, according to several U.S. officials familiar with the meeting.

The administration of the previous president, Felipe Calderón, had granted U.S. spy planes access to Mexican airspace to gather intelligence. Unarmed Customs and Border Protection drones had flown from U.S. bases in support of Mexican military and federal police raids against drug targets and to track movements that would establish suspects’ “patterns of life.” The United States had also provided electronic signals technology, ground sensors, voice-recognition gear, cellphone-tracking devices, data-analysis tools, computer hacking kits and airborne cameras that could read license plates from three miles away.

Under a classified program code-named SCENIC, the CIA was training Mexicans how to target and vet potential assets for recruitment and how to guard against infiltration by narco-traffickers.

In deference to their visitors, the U.S. briefers left out that most of the 25 kingpin taken off the streets in the past five years had been removed because of U.S.-supplied information, according to people familiar with the meeting.

Also unremarked upon was the mounting criticism that success against the cartels’ leadership had helped incite more violence than anyone had predicted, more than 60,000 deaths and 25,000 disappearances in the past seven years.

Meanwhile, Mexico remains the U.S. market’s largest supplier of heroin, marijuana and methamphetamine and the transshipment point for 95 percent of its cocaine.

When the Dec. 15 meeting concluded, Mexico’s new security officials remained poker-faced. “They said they were very appreciative to have received so much information,” said one U.S. official familiar with the meeting. We will be in touch, they added, and left.

Forging ties

U.S. involvement in Mexico’s deteriorating internal security first peaked in the mid-1980s. In 1986, President Reagan signed a National Security Decision Directive instructing U.S. law-enforcement and intelligence agencies to help defeat the growing narco-trafficking menace worldwide.

Beginning in the late 1980s, a massive U.S. air, sea and land effort was shutting down many Caribbean drug routes. The traffickers were increasingly forced to move their product through the only territory left unhindered: Mexico.

Mexico’s secret security ties with the United States date at least to the Cold War, when Mexico City was a hub of intrigue. To keep an eye on the United States, the Soviet Union and China had their largest embassies in Mexico City, necessitating a large CIA presence.

Then the Mexican intelligence service, CISEN, “was basically run by the CIA,” according to one former CISEN official. Although that has changed, the unusually close relationship between Mexican presidents and CIA chiefs has not.

In 2000, the 71-year political rule of the authoritarian and corrupt PRI ended with the election of Vicente Fox of the National Action Party as president. The Sept. 11, 2001, terrorist attacks on the United States turned the new openness into unprecedented bilateral action against terrorism.

The two countries fortified the border with personnel and surveillance technology. Eventually, a protocol was worked out for Mexico to stop, detain and interrogate non-Mexicans traveling north toward the United States. Mexican authorities allow U.S. officials to remotely question third-country nationals of concern to the United States, according to Mexican and U.S. officials.

Clamping down on illegal border crossings, however, had an unintended consequence: It upset agreements among the cartels over smuggling routes, sparking more violent competition.

Death toll climbs

By the time Calderón was inaugurated in late 2006, many experts believed Mexico was losing control of parts of the country. Before his inauguration, Calderón pleaded with President George W. Bush to help the Mexican military quash the cartels, according to Antonio Garza, then U.S. ambassador to Mexico.

Bush agreed to help, and the Merida Initiative, a $1.9 billion aid package for military training and equipment and judicial reform, set the framework for a new level of U.S.-Mexico cooperation. The Office of the Director of National Intelligence took a leading role in the U.S. effort to defeat the cartels.

By then, cartels had begun using assassination squads, according to Guillermo Valdes, director of CISEN at the time. CISEN discovered from a captured videotape and a special analytical group it set up that some of the cartels had hired former members of the U.S.-trained Guatemalan special forces, the Kaibiles, to create sociopathic killers who could behead a man, torture a child or immerse a captive in acid.

To fight back, the CIA proposed electronically emptying the bank accounts of drug kingpins but was turned down by the Treasury Department and the Bush administration, which feared unleashing chaos in the banking system.

As the Mexican death toll mounted, Calderón pleaded with Bush for armed drones. The administration rejected the request because it was far too likely to result in collateral damage, they said.

By 2009, President Obama’s first year in office, horrific scenes had become commonplace in Mexico: severed heads thrown onto a dance floor, a half-dozen bodies hanging from a bridge, bombs embedded in cadavers. Ciudad Juárez, a stone’s throw from El Paso, was a virtual killing zone.

Obama approved an intensification of bilateral measures. Deputy national-security adviser John Brennan led the U.S. side. His Mexican partner was CISEN director Valdes.

Every new program was vetted by Mexico’s security team and often by Calderón.

The first important decision was to use the same “high-value target” strategy that had been successful against al-Qaida in Iraq and Afghanistan. U.S. authorities used real-time intelligence against kingpins on a priority list — including cellphone geolocation, wiretaps, electronic intercepts and tracking of digital records — to help Mexican authorities target them.

The second was to clean up the Mexican units that would be responsible for carrying out raids.

As early as 1997, the DEA had funded the creation of Sensitive Investigative Units (SIU) made up of foreign nationals, first in Colombia, then in Bolivia, Peru and Mexico, and eventually in nine other countries. By mid-2006, the DEA had two units with a total of 184 members in Mexico, according to a DEA inspector general’s report.

Mexico does not allow U.S. agents to take part in the raids, but they can be involved in planning and can direct them remotely. The CIA also has trained units in raid tactics, protection of senior officials, intelligence collecting and in gathering and preserving evidence.

To guard against penetration from the cartels, members were polygraphed, drug-tested and vetted for criminal and financial irregularities. But operations were still routinely exposed by moles. So, beginning in 2009, the size of the units was cut significantly. Those who remained worked under cover and lived in secret safe houses. There are six or seven SIUs in Mexico, sponsored by the DEA, CIA and at least one other U.S. law-enforcement agency.

Quest for drones

The two countries also have constructed an elaborate physical infrastructure and developed protocols for sharing sensitive, often real-time intelligence.

By 2011, the infrastructure extended to a CIA-run fusion center in Mexico City, a DEA-sponsored fusion center in Monterrey, a federal police bunker, also in the capital city, and separate military and federal police intelligence centers and one inside the headquarters of CISEN.

The bulk of the U.S. work finding cartel members depends on the DEA’s network of informants and undercover agents.

DEA-provided information led to the killing of cartel leader Arturo Beltrán Leyva in December 2009. The carte moved significant quantities of cocaine into the United States and had penetrated the highest level of Mexico’s institutions. His death gave Calderón his first significant victory in the anti-cartel campaign.

In another successful mission, the DEA in 2010 located the multiple cellphones of U.S.-born kingpin Edgar Valdez Villarreal, known as “La Barbie” for his Ken-doll good looks. The drug agency tracked his travels over time, allowing Mexican authorities to pursue him through five Mexican states. He was captured in August 2010 and is in Mexican custody, awaiting extradition to the United States.

Drones became part of the mix, too.

U.S. pilots sitting in the U.S. would control the planes remotely, but a Mexican military or federal police commander would direct the pilot within the boundaries of a Mexico-designated grid.

By late 2010, drones were flying deeper into Mexico to spy on the cartels, as they did during the two-day gunbattle involving 800 federal police that resulted in the death of Nazario Moreno González, head of La Familia Michoacana cartel.

By then, Mexican authorities had grown so enamored with drones that they were requesting more flights than the United States could deliver. So Mexican authorities bought their own drones.

Roots of change

In a visit to Washington two weeks ago, Mexico’s top security team shared the outlines of the new plan with U.S. agencies, according to U.S. and Mexican officials. It contains many changes.

The president will not be nearly as directly involved in counterdrug efforts as was Calderón, the officials said. The interior minister will coordinate the relationships among Mexican and U.S. agencies and other Mexican units.

Given the corruption of Mexican law enforcement and armed forces, U.S. officials said privately they would be unwilling to share sensitive information until they have vetted the people involved.

The Mexican government also plans to create five regional intelligence fusion centers and to build a 10,000-member super police force.

This force would be steeped in military discipline but would use police tactics, rather than military force, to keep violence to a minimum.

Medina-Mora, the Mexican ambassador, said in an interview that his nation considers U.S. help in the drug war “a centerpiece” of Mexico’s counternarcotics strategy. But the Mexican delegation also told U.S. authorities that Americans will no longer be allowed to work inside any fusion center.