Secretary of State John Kerry said in a letter to employees that the memories of the Sept. 11 attacks make the day "like none other," and referenced the attacks on the American consulate in Libya a year ago.
"We pause to remember those we've lost and their families, and when we see their friends in the hall, we ask how they're doing," Kerry said in the letter. "My hope is that as we remember our fallen colleagues from both September 11s and all the other sad days, we never forget the reason we do what we do. And though we can't inscribe all their names on a memorial, we also cannot forget the families and loved ones of those who serve and sacrifice in faraway places."
Pipes and drums played at the memorial in New York after the moment of silence, before friends and family members of those who lost their lives read the names of the deceased. A stage honor guard was made up of members of the New York City fire department and police department as well as the Port Authority police department.
For the first responders who rushed toward the World Trade Center12 years ago, the memories of rushing toward the nearly unimaginable tragedy remain strong.
"It's always very difficult this time of year. It brings back somber feelings, time to reflect on your own life," firefighter John Morabito told the TODAY Show on Wednesday. The nationwide memorials help him get through, he said.
"It's extremely powerful, it's an extremely powerful feeling that everyone's thoughts today are on the firefighters and on the rescue workers and on the people, and what we went through in New York City. I was so proud of New Yorkers," Morabito said.
On Tuesday, workers in Shanksville, Penn., broke ground on the Flight 93 National Memorial, beginning construction on the 6,800-square-foot visitor center that will tell the story of Flight 93. Four hijackers turned the plane toward Washington, D.C., likely targeting the U.S. Capitol building, before passengers and crew stormed the cockpit and tried to regain control. The plane crashed into a field and everyone on board was killed.
"Because of the quick and determined actions of the passengers and crew, Flight 93 was the only one of the four hijacked aircraft that failed to reach the terrorists' intended target that day," the National Park Service wrote on its website. "The passengers and crew showed unity, courage, and defiance in the face of adversity."
Organizers announced Tuesday they had raised $40 million, which gave them the green light on the memorial for the 40 passengers and crew members killed. It will include a plaza, a wall of names, memorial groves and a field of honor. The names of the deceased will be read at an observance ceremony Wednesday at 10:03 a.m., when Flight 93 crashed.
The town of Westfield, N.J., planned to hold its annual "We Will Never Forget" ceremony on Wednesday evening to commemorate the 12 residents who died on 9/11. Towns across Connecticut held ceremonies scheduled throughout the day, and Gov. Dannel Malloy declared Wednesday "Honor our Heroes and Remembrance Day."
—NBC News' Sophia Rosenbaum and Matthew DeLuca