A building superintendent in New Brunswick 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 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.