Gil Kerlikowske was hoping to make it through at least his first week on the job without being awakened in the middle of the night. President Barack Obama’s new head of Customs and Border Protection, Kerlikowske could have used a week of quiet as he began to figure out the nation’s largest law enforcement agency, with its 46,000 gun-carrying Customs officers and Border Patrol agents and massive $12.4 billion annual budget. He didn’t get it. On his sixth night after taking office in March, a Border Patrol agent’s single gunshot 1,500 miles away from Washington interrupted Kerlikowske’s sleep. The gunshot itself wasn’t all that surprising; Border Patrol agents regularly open fire on suspected smugglers, border crossers and people harassing them from across the Mexican line. So often, in fact, that the agency doesn’t even bother to release details on most shooting incidents. But this wasn’t a regular shooting incident.

Early the day before, while Kerlikowske, an affable career cop who had spent five years as Obama’s drug czar, was going about his meetings in CBP’s headquarters at Washington’s cavernous Ronald Reagan Building, three Honduran women had surrendered to a green-uniformed U.S. Border Patrol agent in the Rio Grande Valley.

That, too, was a common occurrence. “RGV,” as it’s known in the Border Patrol, has been the epicenter of this year’s “border crisis,” the latest in a long series that stretches back decades—crises that inevitably lead to calls for more money, more agents, more fences. In this year’s iteration, tens of thousands of people fleeing the Central American countries of El Salvador, Guatemala and Honduras have journeyed through Mexico to turn themselves in at the U.S. border seeking asylum. Many of the refugees have been unaccompanied minors (“UACs” to the bureaucracy), a fact that strained the U.S. government response and unleashed critical 24-hour cable media coverage. RGV had been particularly flooded, and so the detention of the three Honduran women—a mother, her 14-year-old daughter and a second teen—around midday on March 12 shouldn’t have been anything other than routine.

Except that they surrendered to Esteban Manzanares.

Manzanares, a stocky 32-year-old agent who kept his head shaved short, was already under suspicion for misconduct—colleagues suspected he had let two border violators go free—but there was a huge backlog of misconduct cases at the inspector general’s field office in McAllen, Texas, and Manzanares was but one small unconfirmed red flag amid many along the southern border, so even under suspicion, he remained on duty with the Border Patrol.

Rather than detain the three Honduran women and bring them to the McAllen holding center, a 300-bed unit that some nights this spring hosted more than 1,000 people, Manzanares locked the women in the back of his Ford patrol truck—and drove them around the scrubland surrounding McAllen for an hour or two. It was a perfectly lovely South Texas day—sunny, low 70s, a bit cool for that time of year.

At 3:15 p.m., Manzanares texted his ex-wife, saying he wanted to be a good dad to their two children: “I want to help in any way I can but I am very limited.”

Then he stopped his truck in a wooded area. He raped both the mother and the daughter. He slit the mother’s wrists and tried to break the daughter’s neck, leaving them for dead in the brush.

He drove off with the third woman bound in his green-and-white heavy-duty Border Patrol truck with a red-and-blue light bar on top, a Department of Homeland Security logo on the door and a U.S. flag on the hood. Somewhere out in the borderlands, the agent left his third prisoner hidden, bound with duct tape.

Manzanares wrapped up his scheduled shift a little after 4 p.m. and returned his truck to the motor pool at the McAllen Border Patrol station, a huge new 68,000-square-foot facility constructed for $22.4 million as part of the agency’s influx of new agents and money over the past decade. Only at 5:45 p.m., his paperwork for the day completed, did he finally pull out of the Border Patrol station. His apartment was just three miles straight down the highway, past South Texas College and then a right turn at the Exxon station, but he wasn’t going straight home.

It was just around that time that other Border Patrol agents made a horrifying discovery, spotting one of the women Manzanares had left for dead wandering past a security camera—one link in the huge post-9/11 network of electronic eyes and sensors that now monitors the border region. Agents responded to the scene and after a brief search located both the injured mother and daughter, took them to the hospital and began looking for their attacker; the women described him as wearing green, so the agents suspected they were looking for one of their own.

They were, and he was not far away: After leaving work, Manzanares had retrieved the third victim and brought her back to his apartment in a housing complex, the last set of buildings before the Rio Grande that demarcates the two countries. The complex was home to a number of his Border Patrol colleagues—including his next-door neighbor and one across the hall. They all joked about how safe it was. Border Patrol agents seemed to be everywhere in McAllen these days, as the agency since 9/11 had become one of the region’s largest employers, a boon for one of the poorest metropolitan areas in the country. There were now some 3,200 agents in RGV—driving along the border, patrolling by boat, flying overhead in helicopters, working interior checkpoints, watching cameras, staffing the Border Patrol’s new overhead surveillance blimp, the latest high-tech toy cast off by the Pentagon and repurposed to protect the border.

Back inside his apartment, Manzanares stripped his teenage prisoner naked, bound her to a chair, stuffed a sock in her mouth and raped her.

By 7 p.m., the Border Patrol, having questioned the first two victims, had realized there was a third victim, notifying the FBI that a kidnapping had occurred and that the girl was probably being held by a Border Patrol agent. The magnitude and horror of the crime were unusual, but the potential perpetrator wasn’t. The FBI in McAllen had gotten used to investigating assaults and misconduct among Border Patrol agents; it had become the field office’s top criminal priority.

It took only hours to narrow down a suspect: When investigators examined the truck Manzanares used on his shift, they found blood and duct tape.

By 12:39 a.m., FBI agents knocked on his red door, Apartment 1513, and shouted, “FBI—federal agents.” At first, there was no response. Then, the agents heard a single gunshot as Manzanares took his own life. When a SWAT team broke down the door, they found the teen inside, still naked and bound, but alive.

Now it was definitely time to tell the new commissioner.

Kerlikowske had already known that the Border Patrol was troubled, of course: It had taken 1,870 days into the Obama administration before he even became the first Senate-confirmed commissioner of the Obama era, and he was well aware he didn’t have much time to right an agency that was beset by corruption problems and excessive force complaints, the unfortunate legacies of a massive hiring surge that had doubled the force’s size in just a few years after 9/11. That lying and obfuscation had often accompanied the scandals was no real surprise either.

“We had a history of not addressing things as directly as we should,” Kerlikowske told me when we met this fall in his office at the Reagan Building.

Kerlikowske wanted to use the Manzanares attack as an opportunity to show that on his watch, the agency would be different—more forthright and transparent. But it wouldn’t be easy: He wrote a first draft of a statement he wanted to send out immediately, but CBP officials blocked their own new commissioner. They were nervous about admitting fault so quickly. CBP’s longstanding policy had been to hold off for days, weeks, months and even years before addressing publicly any misconduct incident.

The CBP leadership was so concerned about Kerlikowske’s statement that he finally had to turn to the new secretary of Homeland Security, Jeh Johnson, and the new DHS general counsel, for their approval.

Two days later, CBP released Kerlikowske’s statement, the first since his swearing-in as commissioner. “I consider these actions, if true, to be reprehensible and I know they are not representative of the agents of the U.S. Border Patrol,” it said. “I am deeply sorry that this incident occurred and am committed to doing everything in my power to prevent incidents like this from occurring again.”

Anywhere else it would hardly have seemed like a controversial thing to say under the circumstances—but this wasn’t anywhere else. And Kerlikowske had to start somewhere.

***

The United States today spends more money each year on border and immigration enforcement than the combined budgets of the FBI, ATF, DEA, Secret Service and U.S. Marshals—plus the entire NYPD annual budget. Altogether, the country has invested more than $100 billion in border and immigration control since 9/11.

It has paid for quite a force: Customs and Border Protection not only employs some 60,000 total personnel—everything from desert agents on horseback to insect inspectors at airports—but also operates a fleet of some 250 planes, helicopters and unmanned aerial vehicles like the Predator drones the military sent to Iraq and Afghanistan, making CBP both the largest law enforcement air force in the world and equivalent roughly to the size of Brazil’s entire combat air force.

The Border Patrol wing of this vast apparatus has experienced particularly dramatic growth: By the time the Bush administration left Washington, the fiercely independent agency—part police force, part occupying army, part frontier cavalry—had gone from being a comparatively tiny, undermanned backwater of the Justice Department to a 21,000-person arm of the largest federal law enforcement agency in the country.