The city and the nation paused Thursday to remember those who died at the World Trade Center, the Pentagon and in Shanksville, Pennsylvania 13 years ago.
Families of the victims of the September 11th attacks gathered at the World Trade Center Memorial Plaza in Lower Manhattan to pay their respects.
The first ringing of the bell occurred at 8:46 a.m., the exact time the first plane hit the Twin Towers.
Moments of silence were observed for each moment the planes struck and at the times the towers fell.
Mourners left flowers, flags, and other mementos by the names of loved ones.
Many also participated in the reading of the names.
The memorial was open only to family members earlier in the day before it opened to the public again at 6 p.m.
This was also the first year that the National September 11th Museum is open on the anniversary of the attacks.
"This is a chance for families either during or after the ceremony to go down into the museum to really see the lives that were lived," said 9/11 Memorial President Joe Daniels.
As always, the stepped-up security provided a reminder that 13 years later, the terror threat looms as large as ever.
"People living in this city, people visiting this city should be aware of the threat of terrorism but should not be living in fear of it," said Police Commissioner William Bratton.
Of the 2,753 victims killed at the World Trade Center, more that 400 were first responders.
"You couldn't say that it heals. I guess it's like a really bad burn. It gets scarred over. It gets uncomfortable and it's itching, but it is not that horrible pain we had for so long immediately afterwards. Time does help," said Former FDNY Commissioner Thomas Von Essen.
"The emergency workers - police, firefighters, EMS - a significant number of those lost along with thousands of civilians. A poignant day, and for those of us living in the city that day, a special poignancy," Bratton said.
Precincts in all five boroughs held roll call for the 23 members of the NYPD who were killed during the terror attacks.
Officers bowed their heads in silent remembrance as the entire list of names was read.
City, state and national officials - both past and present - were also on hand for Thursday's solemn ceremony. For Mayor Bill de Blasio, it was his first anniversary ceremony as mayor. Governors Andrew Cuomo and Chris Christie were also present, as well as Homeland Security Secretary Jeh Johnson.
As for the site itself, progress continues. One World Trade will soon accept tenants, the transit hub is rising, and the 9/11 Museum is complete.
Ceremonies were also held in the nation's capital on Thursday.
Staff members lined the White House lawn, joining President Barack Obama, First Lady Michelle Obama and Vice President Joe Biden.
A moment of silence was held at the times of each of the four plane impacts.
The president also attended services at the Pentagon where he commented on the importance of sharing the story of 9/11 with future generations.
"Beginning tomorrow there will be teenagers, young adults, who were born after 9/11. Though these young Americans did not know the horrors of that day, their lives have been shaped by all the days since. A time that has brought us pain, but also taught us endurance and strength: A time of rebuilding, of resilience, and of renewal," Obama said.
The president was joined at the ceremony by Secretary of Defense Chuck Hagel and General Martin Dempsey.
Hundreds of family members gathered in Shanksville, Pennsylvania to honor the 40 people who died there on September 11, 2001.
A granite memorial now sits in the field at the site where Flight 93 went down.
A Congressional Gold Medal was awarded to the passengers and crew members who fought hijackers.
Pennsylvania Governor Tom Corbett spoke about how September 11th changed the history of Shanksville.
"Thirteen years ago on this date it became a new battlefield, here in this country, in the war on terror though, as compared to other wars we have fought. Today it is truly a monument and a place with trees, with granite, with winds and memories," Corbett said.
The former speaker of the house donated the American flag that was flying that day on top of the Capitol building where Flight 93 might have ended up if the passengers had not rebelled.