On a clear summer day, Lieutenant Isa Abbassi and Officer Jamal Kilkenny are taking in the sights, NYPD-style. Their Agusta A119 helicopter, bearing the NYPD’s distinctive blue and white markings, soars 700 feet above the East River, its single engine purring at top speed. Heading north at 70 miles per hour, the chopper whirls by the Brooklyn and Williamsburg Bridges as Kilkenny points its L-3 Wescam multisensor camera at various tourist destinations: the South Street Seaport, the United Nations’ headquarters, the 59th Street Bridge. Fifteen minutes later, the chopper circles the Staten Island Ferry and the Statue of Liberty, scanning the statue’s base for anything suspicious—for example, the wrong boat in the wrong place or scuba divers off Lady Liberty’s dock.

Abbassi and Kilkenny also check out sites that the public doesn’t visit—the army base at Fort Hamilton in Brooklyn; the alleys, warehouses, and storage areas near LaGuardia and John F. Kennedy Airports; a power plant in Queens; the giant ventilator shafts that aerate the Holland and Lincoln Tunnels; and the entrance in Queens to the Buckeye Pipeline—which carries millions of gallons of jet fuel to JFK and which was the target of a foiled Islamist terrorist attack in 2007. From time to time, Kilkenny monitors his radiation detectors, technology so sensitive that it sometimes mistakes crates of potassium-rich bananas for nuclear material. It takes just 25 minutes for the chopper to circumnavigate the five boroughs of New York and the more than 100 “critical locations” that the 62-person aviation unit patrols day and night.

The NYPD’s fleet now has seven helicopters: four Agusta A119s and three Bell 412s, larger twin-engine choppers that can transport 15 SWAT-team members to a rescue scene. The aircraft contain an arsenal of monitoring equipment powerful enough to read a license plate or the name of a book in a pedestrian’s hand almost a mile away. Their satellite navigation system lets pilots zoom in on any location simply by typing in an address on a keyboard, while their giant strobe lights can turn night into day on dark rooftops or bridges. The choppers also have compartments for .50 caliber swiveling machine guns and other heavy weapons. Such capability isn’t cheap: the Agustas cost $4.5 million apiece, and the Bells $14 million. But Police Commissioner Raymond W. Kelly says that the aviation unit is vital to protecting New York City from terrorism. “We could not cover this much territory in such depth so quickly and thoroughly any other way,” Kelly says.

The fleet’s size, activity, and capabilities make it a good symbol of the NYPD’s relentless focus on counterterrorism since the attacks of September 11, 2001. No other city in America has a comparable fleet; then again, no other city faces comparable danger. Since 2001, at least 11 serious plots against New York have failed or been thwarted, police say. Preventing another terrorist catastrophe is Kelly’s paramount mission. A decade after 9/11, the NYPD has adapted to the challenge and become not just the nation’s most highly regarded police department but the nation’s most effective counterterrorism force.

The extent of the NYPD’s fight against terrorism is enormous. Few New Yorkers know that each of the department’s 76 precincts dedicates at least one patrol car to routine checks on houses of worship and other sites that terrorists might try to strike. Or that Kelly allocates some $330 million of his $4.6 billion annual budget to counterterrorism-related activities, with 1,200 of his 50,000 employees assigned to the war on terror. Or that he has continued to give priority to counterterrorism during the budget-mandated shrinkage of his force, which now has about 10 percent fewer officers than it did in 2001. (The force has still achieved a 40 percent drop in serious crime since Kelly returned to the commissioner’s job in 2002.)

A recent demonstration of the NYPD’s ongoing engagement with terrorism came on May 1, after Navy SEALs killed Osama bin Laden in Pakistan. The audacious raid, Kelly told his top aides, was “good news—with complications.” Those complications included the possibility that some of bin Laden’s followers would seek to avenge his death by attacking the global jihad’s top target: New York. By the time President Obama made the late-night announcement that bin Laden was dead, a message instructing police officers to prepare for trouble had already gone out to all commands, and precincts were heightening security around station houses and the city’s iconic sites. A midnight tour of cops working transit hubs was held over, almost doubling the number of officers deployed in subways and around the city’s train and ferry stations. The next morning, New Yorkers on their way to work found extra police, bomb-sniffing dogs, and bag-check posts in subway and train stations; a similar increase was ordered for the evening rush hour.

Some of those emergency measures remained in force weeks later, as the heat of summer began. While Secretary of Homeland Security Janet Napolitano stressed that her agency had received no warnings that would elevate its now colorless alert system to a higher level, Kelly continued to believe that the threat to New York had increased, at least in the short run. “Threats to New York keep coming out in bin Laden’s notes,” Kelly tells me. So far, the material that the SEALs plucked from bin Laden’s Abbottabad compound has not revealed the existence of a specific plot aimed at New York, a senior official in Washington says. But the material apparently does show that bin Laden kept thinking about how to attack Gotham. References to New York—as well as to Chicago, Los Angeles, and other leading American destinations—show up repeatedly in the documents, photos, e-mails, and other material that the CIA and other intelligence agencies are currently analyzing.

Ray Kelly begins each working day with a briefing on terrorist trends from two top aides: David Cohen, his chief of intelligence and a former chief of the CIA’s operations division; and Richard Daddario, his deputy for counterterrorism. Since early June, the sessions have taken place in Kelly’s sleek new Executive Command Center on the 11th floor of One Police Plaza, the department’s dilapidated 1970s-era headquarters overlooking the Brooklyn Bridge. From 9 to 10 am, the three men sit at the center’s long oval table and pore over reports of terrorism incidents at home and abroad; ongoing investigations; splits and internal ideological shifts in militant jihadist groups; and developments in Iraq, Afghanistan, and elsewhere. As they talk, television broadcasts fill the giant wall-to-wall screens that surround them—Al Jazeera in English and Arabic; New York

One, which monitors developments in the city; breaking news from Fox, MSNBC, and CNN; and alerts from the all-important Weather Channel. The screens can also display live video feeds from some 200 subway cameras and from the NYPD’s helicopters. The windowless room, which can seat up to 40, is “secure”: with its own independent air and electrical supply, officials can seal it off in an emergency.

On a typical morning, a police source says, Cohen outlines reports from the department’s 11 overseas liaisons—detectives embedded in local police forces in London, Lyons, Jerusalem, Amman, Singapore, and other terrorist hot spots. The presence of the department’s eyes and ears abroad has occasionally rankled the Federal Bureau of Investigation, which has its own extensive network of overseas agents. But Kelly insists on receiving terrorism-related information in a timely manner. “This was our way of ensuring that the New York question in any terror investigation is always asked,” says Paul Browne, the deputy commissioner for public information and Kelly’s long-standing confidant.

One morning in June, the official says, the trio discussed the commissioner’s plans for the NYPD’s World Trade Center Command, a temporary post of 200 to 240 cops and support staff assigned to protect the new memorial at Ground Zero, which is scheduled to open on the tenth anniversary of 9/11. Eventually, says Kelly, as many as 700 officers may be assigned to secure the 16-acre World Trade Center site, which, as currently configured, will house the 9/11 memorial, five towers, an arts center, and a transit hub that the NYPD will police in cooperation with the Port Authority of New York and New Jersey, which owns much of the land. Terrorists have already attacked the World Trade Center twice, of course, and in 2006, the police disrupted a plot to bomb a train tunnel and a retaining wall at Ground Zero. Browne calls the site the “Number One target in the city that remains the nation’s top target.”

Unsurprisingly, many of the department’s most ambitious counterterrorism undertakings aim to enhance security in lower Manhattan. In November 2008, Kelly quietly opened a high-tech command center in a nondescript downtown office building to monitor 150 closed-circuit cameras, 30 license-plate readers, and other sensors operating around Wall Street; within a year, there may be as many as 1,500 public- and private-sector cameras in operation downtown, Kelly says, all of which the NYPD can access. This is the Lower Manhattan Security Initiative, modeled in part on the “Ring of Steel,” a surveillance system set up in London’s financial district after terrorists there killed 56 people and wounded more than 700 in 2005. But New York’s version exceeds London’s in sophistication and scope. The New York cameras, for instance, are programmed with an algorithm that instructs them to send an alert when a package or briefcase is left unattended for too long or when people make certain physical movements, which the NYPD declines to discuss.

Last September, Mayor Michael Bloomberg announced that the NYPD and the Metropolitan Transit Authority were extending the Lower Manhattan Security Initiative into midtown Manhattan. Ultimately, some 1,500 more cameras, license-plate readers, and environmental monitors will be integrated into the system. The cameras are now installed in some of the city’s busiest transport hubs—Grand Central Terminal, Penn Station, and the subway station at Times Square. Washington will pick up virtually all of the security initiative’s $200 million tab.

These projects have alarmed some civil libertarians. Donna Lieberman, executive director of the New York Civil Liberties Union, has wrangled with Kelly’s NYPD over a myriad of issues, including its “stop and frisk” policies; spot checks of backpacks, handbags, and briefcases in subways; and surveillance tactics used to protect the Republican National Convention in 2004. She accuses the department of trying to turn New York into a “surveillance society” in which “every move you make is recorded by the police department and no one knows if there are rules in place to protect privacy or sufficient independent oversight of the system.” In September 2008, the NYCLU sued the police in the state’s supreme court for refusing to disclose information about how the Lower Manhattan Security Initiative would safeguard privacy. In June of the following year, it filed a federal lawsuit against the Department of Homeland Security, seeking to learn, among other things, how the police and Washington planned to use the information and with whom they planned to share it. Both lawsuits are still pending.

Browne says that the surveillance system has strict privacy safeguards. The pictures and data collected won’t be stored for longer than 30 days unless they’re part of an ongoing investigation, he notes. Further, he says, several agencies and individuals have the authority to investigate potential wrongdoing in the camera project and in the NYPD’s other counterterrorism programs: five district attorneys, two U.S. attorneys, and an independent Civilian Complaint Review Board, not to mention the city council’s oversight committees on finance and public safety.

Cohen says that similar safeguards apply to the deployment of undercover cops who infiltrate suspected terrorist groups—the heart of the NYPD’s intelligence-collection effort. “At virtually every meeting, we have a legal counsel who oversees ongoing investigations,” he says. Both deputies deny the assertions of some Muslim activists, who have charged that the department discriminates against Muslims by performing undercover surveillance in mosques when not pursuing particular leads in an investigation. “We don’t target mosques,” says Browne. “We follow leads.”

However, two recently published reports have raised questions about whether the NYPD’s surveillance of Muslim individuals and groups violates federal civil liberties and privacy laws. Last month, the Associated Press reported that the NYPD had targeted ethnic communities “in ways that would run afoul of civil liberties rules if practiced by the federal government.” It also questioned the department’s relationship with the CIA, alleging that the NYPD’s intelligence division’s employment of CIA officials, as well as its undercover activities, had “blurred the line between foreign and domestic spying.” The NYPD strongly denied the reports, saying that no spying had occurred without a criminal lead.

But this week, NYPD Confidential, a well-read blog among law enforcement officials, published an internal NYPD intelligence-division report challenging the NYPD’s assertion that it only follows tips. The 2006 document, according to the blog, showed that the police had compiled information on 250 mosques; 12 Islamic schools; 31 Muslim student associations; 263 places called “ethnic hotspots,” such as businesses and restaurants; and 138 “persons of interest.” Together, the reports could prompt more calls for federal and independent oversight of the NYPD’s counterterrorism activities.

While much of the press coverage of the NYPD has focused on the department’s cutting-edge technology—Kelly is a self-confessed “gadget guy”—he and other senior officials insist that the department’s true strength in fighting terrorism is its people. “The continuity of leadership is key,” says Cohen. “I’m in my tenth year in this job,” he says; so are at least half of the counterterrorism division’s employees. “There is no supervisor who doesn’t understand the mission; they are expert at what they do.”

Another personnel advantage is the NYPD’s diverse makeup, which mirrors the city’s own. Kelly points out that the department’s recruits over the past five years were born in 88 different countries. The chopper pilots who flew me around the city are a case in point: Abbassi, head of the department’s aviation unit, is of Arab descent; Kilkenny’s family, despite his Irish surname, is from Guyana. This diversity gives the NYPD an enviable language capability and an edge in its undercover work, recruitment of informants, informal neighborhood surveys, and cyber-unit, which monitors radical websites in several languages. Not even the FBI’s linguistic depth and range are as great, Kelly asserts.

The terrorism threat has evolved sharply since early 2002, when Kelly first sketched out his plan for countering it on a piece of paper for Mayor Bloomberg. Al-Qaida’s “core,” as counterterrorism experts call the organization that bin Laden headed, does remain a threat. U.S. intelligence officials guess that more than two-thirds of its leadership cadre have been killed or jailed during the past decade, but underestimating the organization could still be disastrous. Last May, Steve Kappes, a former deputy CIA director, told an NYPD gathering of public and private security professionals that al-Qaida was the “most adaptive terrorist entity” he had encountered in his 30-year intelligence career. Even without bin Laden, he said, its threat might not be “significantly diminished” for years to come.

Another danger is the expansion of what Bruce Hoffman, a terrorism analyst at Georgetown University, calls the “al-Qaida universe.” In 2008, there were seven al-Qaida networks or theaters of operation; last year, there were 11. Such groups find political vacuums in failed and failing states very attractive. Al-Qaida in the Arabian Peninsula, or AQAP, has grown increasingly lethal and ambitious in Yemen; in Somalia, al-Shabaab has attracted several young Somali-Americans to its ranks from Minnesota, of all places.

Among the most ominous recent trends is the surge in “homegrown” terrorism, which was initially identified in 2007 by NYPD analysts Arvin Bhatt and Mitchell Silber. That threat came home dramatically to the NYPD in 2004, when it arrested two immigrants, Shahawar Matin Siraj and James Elshafay, for planning to bomb the Herald Square subway station during the 2004 Republican National Convention. Elshafay cooperated with prosecutors and got a plea deal; Siraj was convicted on four counts of conspiracy and received a 30-year prison sentence. The fact that Siraj had emigrated as a child from Pakistan, had grown up in the United States, but still wanted to kill Americans made a strong impression on the police department, Cohen recalls: “It was the first homegrown case against a U.S. target that resonated so deeply.” Homegrown terrorism captured headlines again in May 2010, when Faisal Shahzad, a naturalized Pakistani-American and middle-class Connecticut resident, tried to blow up his SUV in Times Square. Only luck and his insufficient training kept Shahzad from carrying out his martyrdom mission, the police concede.

The homegrown trend has severely complicated counterterrorism efforts. In 2009, at least 43 American citizens or residents were charged with terrorism crimes, according to Hoffman’s count; last year, the number was at least two dozen. At a counterterrorism meeting in New York last winter, Silber warned that more homegrown plots would be likely in the near future, not just in the United States but in Europe, Canada, and Australia as well. In fact, he said, the preponderance of major terrorist plots against Americans since 9/11 have been homegrown, and between 2004 and 2009, 90 percent of the “core conspirators” of jihadist plots against the West were radicalized in the West. While al-Qaida remains a serious problem, Silber argues, the threat today comes mainly from “younger Muslim men between the ages of 15 and 35” who are middle-class and have no direct al-Qaida connection but have been radicalized by an “extreme and minority interpretation” of Islam. Brian Jenkins, a veteran counterterrorism guru at the RAND Corporation, says that a related problem is the emergence of “do-it-yourself” terrorism, more diffuse and less predictable than centrally directed plots.

What keeps Kelly and his team awake at night? Not the historical rivalries and resentments between the FBI and the NYPD, they say. Kelly maintains that the two organizations now work together well. The police department once had only 12 detectives on the FBI’s Joint Terrorism Task Forces; today, it has 120. “The major source of information for us is the JTTF,” Kelly says. Cohen agrees: “Cooperation today between the police and the JTTF is standard operating procedure.” Of course, the department still gets annoyed when the FBI decides not to pursue an investigation developed by the NYPD or asserts jurisdiction over one that the NYPD wants to lead.

The NYPD has also negotiated protocols with other city agencies that often figure in terror investigations—New York’s vast public-health service, for instance, the police department’s partner in efforts to hunt down pathogens and viruses that could be used in a terrorism attack. But Kelly does worry about what he and his counterterrorism division cannot control unilaterally—for instance, the policing and protection of bridges, tunnels, and the Hudson River, whose surveillance is shared with the Port Authority and the Metropolitan Transit Authority. A related concern is the inability or unwillingness of neighboring jurisdictions to implement counterterrorism measures similar to New York’s—one reason for the NYPD’s Sentry program, which trains cops in the tristate area in counterterrorism techniques in order to foster intelligence-sharing.

And, of course, Kelly worries about an attack using nuclear weapons or other WMDs. Daddario, the counterterrorism division chief, has thought long and hard about how New Yorkers would evacuate the city in the event of a widespread biological or nuclear attack. The NYPD has drawn up evacuation plans, but they’re of limited value, he says; in such an emergency, the police department would have to rely on “self-evacuation”—individual decisions by hundreds of thousands of New Yorkers to leave the city, even on foot and across bridges. Daddario also admits that the state-of-the-art air sniffers that are supposed to detect anomalous airborne pathogens need improvement. “The technology is not there yet,” he says.

Another terrorism-related anxiety for Kelly, aides say, is that the government’s visa policies and the country’s easily penetrable borders mean that he doesn’t know who’s living in New York. In 2005, Congress passed the REAL ID act, requiring states to issue driver’s licenses that could be readily authenticated through encryption and biometrics after a background check. But many states have rebelled against implementing it, citing cost, privacy, and other concerns. It’s hard to protect the nation, warned former White House terrorism advisor Richard Clarke in his 2008 book Your Government Failed You, if the government doesn’t know who is in it.

Perhaps the greatest challenge to the NYPD’s efforts, however, is the way we think about terrorism. “Americans like to see conflicts as finite, with a beginning and an end,” says Jenkins. “But that will not be the case in the struggle against terrorism. This challenge adapts and morphs and is constantly evolving. It won’t end. It’s hard for any individual or government agency to accept that.” Even in New York.

Photo by Jose Jimenez/Primera Hora/Getty Images

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