It’s been more than four years since I first wrote in detail about the way the New York City Police Department and the Central Intelligence Agency work together in Securing the City: Inside America’s Best Counterterror Force—the NYPD. Since then, some new facts have emerged, most recently in The New York Times report Wednesday about the CIA’s internal investigation of the links. But the questions I raised in 2009 remain the most important ones to be answered.

The most basic of all is simply this: “How do you stop terrorists?” There are not very many of them, despite popular perceptions, and a lot of those are stupid. But as we saw recently in Boston they can have a huge impact on the national psyche and the global news cycle. When they have succeeded in mounting really big operations, 9/11 in 2001, the Madrid bombings of 2004 and the London bombings of 2005, they have changed the course of history.

Throughout the George W. Bush administration I watched the “Global War on Terror” destroy American credibility and do very little to eliminate terrorists while doing a hell of a lot to win them new recruits. We were told we were “fighting them over there so we don’t have to fight them here.” But it was clear that our troops, our money, and our morals were being thrown away on a fool’s errand occupying Afghanistan and Iraq.

What were the alternatives? The first stock answer to that was “law enforcement,” treating terrorists as mere criminals, chasing them down, bringing them to trial, just like in the good old days. You’d take into account all the fundamental qualms and constitutional caveats inherent in America’s traditional view of civil liberties and that would make us safe from the bad guys out there and from our own government at home. But clearly after 2001 we were no longer in the good old days. And, while people feel less threatened by terrorism in 2013 than they did in 2003, we’ll never be able to turn back the clock completely.

What fascinated me about the NYPD’s approach to fighting terrorism was that it developed what was, essentially, a third way that combined the power of law enforcement and the reach of a global intelligence network. This was done despite running feuds and turf battles with agents of the FBI, and it was made possible in large part because of some very special and sometimes unsettling cooperation with the CIA.

It should be obvious that if your goal is simply to punish terrorists after the fact, you won’t be doing a very good job protecting people in your country or in your city. In the age of suicide bombers the threat of a prison term is not only no deterrent, it’s irrelevant.

So what’s needed is solid real-time information that allows you to identify terrorists before they act and—this was a particularly interesting but iffy wrinkle in the NYPD approach—sometimes before they even know themselves that they are terrorists. The next issue, once they are identified, is to dissuade them or disrupt their plots using tactics of recruitment, intimidation, deception, and—in some cases—force. Only rarely do you make arrests, because those expose your operatives and your methods when the case goes to trial.

“With local law enforcement,” New York Police Commissioner Ray Kelly told me in 2008, “you have more flexibility in recruiting confidential informants, and obviously in arresting people. The whole package is in one agency.” The operative word is “flexibility.” And when that “agency,” the NYPD, has more than 35,000 sworn officers of the law in a city of 8.5 million people, 40 percent of whom were not born in the United States, there’s a lot of potential to gather information. If hundreds of your cops come from immigrant backgrounds themselves and speak languages like Arabic, Urdu, and Farsi with native fluency, that helps, too.

Several people were at the center of the NYPD-CIA relationship in its formative years, but the most important was and remains David Cohen, who has been the department’s deputy commissioner for intelligence since 2002. Cohen, a lanky gray-haired man with a strong working-class Boston accent, previously headed the CIA’s clandestine services. Perhaps even more relevant to the questions being raised today, he was instrumental in reorganizing the agency’s operations inside the United States in the late 1980s.

Notwithstanding journalistic and government boilerplate about there being no CIA-in-the-USA activities, the agency has fairly extensive intelligence-gathering functions in America, and it used to have two somewhat distinct operations: one focused on interviewing academics, businessmen, and others coming back from travels abroad in problematic areas (especially during the Cold War); the other established CIA stations in cities like Detroit with large immigrant populations where “agents of access” could be recruited who would help the CIA gather human intelligence from their relatives, friends, and acquaintances in foreign countries. Some members of the Lebanese community in the United States, for instance, provided vital links for the agency’s operations targeting Hezbollah’s activities around the world. What Cohen did at the CIA was consolidate those two operations, which of course put him at odds with many FBI agents, who thought he was poaching on their turf.

Cohen had spent most of his CIA career as an analyst before moving over to that darker side of the agency, then known as “operations” and now known as “clandestine services,” and he rose up through its ranks at a time when Langley was imploding.

The discoveries that two of the CIA’s own people, Aldrich Ames and Harold Nicholson, had spent years spying for the Russians had led to a wholesale purge. And as veteran operatives quit or were forced out, Cohen moved up.

At the time, an FBI agent named Edward J. Curran was in charge of the internal CIA investigation that many insiders saw as a witch hunt. Subsequently, Cohen recruited Curran for the NYPD, where he has spent years running liaison with foreign police forces and intelligence operations. NYPD detectives are stationed in Tel Aviv, London, Paris, and several other cities around the globe for just that purpose.

Cohen ended his active career at the agency in the late 1990s with a post as the head of the CIA’s New York office, which has a wide array of functions in a city that hosts many global organizations, including, of course, the United Nations. At the time, an FBI agent named Sidney Caspersen was in charge of the Feds’ “electronic surveillance” in the city. Caspersen also eventually went to work for Cohen at the NYPD.

Meanwhile, Cohen maintained close ties to many of his old colleagues in the top ranks of the agency. These included George Tenet, the CIA director in the early Bush years, and John Brennan, who’s the CIA director now. Brennan, like Cohen, had spent most of his agency career as an analyst, but Cohen moved him to operations and appointed him to be the CIA station chief in Saudi Arabia back in the mid-1990s. Brennan was President Barack Obama’s deputy national-security adviser for homeland security and counterterrorism before taking his current post.

One of the most interesting spooks to join up with the NYPD was undoubtedly Lawrence Sanchez, a veteran of the CIA’s clandestine services whose name was blanked out of the CIA inspector-general’s report on relations with the department, but whose career I covered extensively in my book.

Sanchez was sent to the NYPD under the authority of the Directorate of Central Intelligence “to improve analytic information-handling capabilities of law enforcement entities in the States of New York and New Jersey,” according to the inspector-general report. In fact, as I reported in 2009, he was a conduit channeling CIA intelligence from abroad to the New York police so they could act on it much more quickly than if they had to wait for the usual FBI-controlled bureaucracy to deliver the information.

(“Listen to this,” Cohen told me one morning in 2008 at his office in downtown Manhattan. “We got a report from the FBI on the Madrid bombing which was terrific, it was great … It was f--cking 18 months later!” He drank from a mug with the eagle-and-compass seal of the CIA on it. “They tried the best they could,” he said.)

Sanchez liked it at the NYPD, and when his temporary assignment ended he got permission to continue working in New York on unpaid leave. During this period, Sanchez “did not consider himself an agency officer and believed he had ‘no limitations’ as far as what he could or could not do,” according to the inspector general.

That’s for sure. Cohen believed that in the real world of intelligence operations, there’s no such thing as “sharing,” there’s only “trading,” and part of Sanchez’s brief was to use New York as a kind of window on the world where information could be gathered and agents of access recruited to learn more about developments abroad, much like the operations in Detroit in the 1980s. But unlike the CIA, the police have the power to pick up people for relatively minor offenses, outstanding warrants and such, then turn them into informers. This is a tried-and-true tactic of crime fighting that the NYPD could use for the purposes of preventing terrorist attacks. It could also gather intelligence to be traded in that shadowy barter economy of espionage.

But Sanchez went even further. In 2007, as a senior NYPD official, Sanchez testified on Capitol Hill before a sympathetic Senate Committee on Homeland Security and Governmental Affairs. “Wearing a yellow tie (what used to be called a ‘power tie’), his biceps visibly bulging beneath this gray business suit, Sanchez put a very particular and unabashedly paternalistic spin on the role of the NYPD,” as I wrote afterward. “Rather than just protecting New York City citizens from terrorists,” he said, “the New York Police Department believes part of its mission is to protect New York City citizens from turning into terrorists.” In other words, the police would save Muslims from themselves.

Sanchez is now in private business and no longer with the NYPD or, I think, the CIA.

All of this made me uneasy when I was writing the book, and it makes me uneasy now. I keep coming back to that basic question, “What are the alternatives?” I have yet to find an answer that really seems satisfactory. But for 12 years now, it should be said, New York City has been secure.