By MATT APUZZO and ADAM GOLDMAN   08/24/11 06:10 AM ET   

NEW YORK — In New Brunswick, N.J., a building superintendent opened the door to apartment No. 1076 one balmy Tuesday and discovered an alarming scene: terrorist literature strewn about the table and computer and surveillance equipment set up in the next room.

The panicked superintendent dialed 911, sending police and the FBI rushing to the building near Rutgers University on the afternoon of June 2, 2009. What they found in that first-floor apartment, however, was not a terrorist hideout but a command center set up by a secret team of New York Police Department intelligence officers.

From that apartment, about an hour outside the department’s jurisdiction, the NYPD had been staging undercover operations and conducting surveillance throughout New Jersey. Neither the FBI nor the local police had any idea.

Since the terrorist attacks of Sept. 11, 2001, the NYPD has become one of the country’s most aggressive domestic intelligence agencies. A months-long investigation by The Associated Press has revealed that the NYPD operates far outside its borders and targets ethnic communities in ways that would run afoul of civil liberties rules if practiced by the federal government. And it does so with unprecedented help from the CIA in a partnership that has blurred the bright line between foreign and domestic spying.

Neither the city council, which finances the department, nor the federal government, which contributes hundreds of millions of dollars each year, is told exactly what’s going on.

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