City officials and Navy officers stood at attention in a solemn, wordless ceremony as an honor guard of police officers and firefighters lifted the flag and bagpipers played "America the Beautiful."
On Sept. 11, firefighters Dan McWilliams, George Johnson and Billy Eisengrein were photographed as they raised the flag above the smoldering rubble.
"The flag has special meaning," Fire Commissioner Nicholas Scoppetta said before the ceremony. "It seemed to represent an indomitable spirit, a coming back from those attacks."
The flag was sent to the USS Theodore Roosevelt in October as it sailed toward Afghanistan. It has since flown on six other Navy ships.
It was returned to New York last week after a ceremony aboard the Roosevelt as it ended its six-month mission and returned to Norfolk, Va.
At Monday's ceremony, Mayor Michael Bloomberg and other city officials were joined by McWilliams, Johnson and Eisengrein.
Afterward, Eisengrein had little to say about his role.
"It was just three New York City firefighters who raised the flag," he said.
The flag will fly over City Hall for one week, and then will likely circulate among city police stations and firehouses in a case crafted by the Navy, said Michael Handy, director of the mayor's Office of Veterans Affairs.