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.