On September 11th, 2001, I was relatively new to New York as a lower Manhattan professional. I was on my way to work from Bay Ridge, Brooklyn on the R train, which travels under the World Trade Center. During the ride to work that day, someone pulled the emergency cord and stopped the train just before it traveled under the World Trade Center, and shortly before the reported time of the planes hitting the towers. The train operator thought it was a "medical emergency" and after it was deemed ok to continue, someone pulled the cord again, stopping the train once more.
Passengers were told to change trains and attempt to reach Manhattan by backtracking to Brooklyn and taking another train line. When some of us got on the Brooklyn bound train, the passengers coming from Manhattan were yelling about something that had just happened in Manhattan, and I remember someone frantically telling us "papers were flying around in the air". When I finally reached my stop in Manhattan(one! stop after the World Trade Center stop), there was an announcement in the subway that "If you work in the World Trade Center, turn around and go home."
I exited the subway anyway, tried to get into my office in the Federal Building, but was not allowed near the building. There was a big black cloud of smoke, and many people were outside observing it. We heard a plane, and someone screamed "it's another one, it's another one" and it seemed like all of New York went running north. I ended up walking across the 59th street bridge with other New Yorkers, and we had no idea whether the events of the day were over. It took five hours to get home to Bay Ridge, Brooklyn that day.