Mayor Eric Adams, who continues isolating after testing positive for COVID-19, presided virtually over the ceremony.
"Today, I want to thank some of the heroes who were there on the scene," he said. "We're going to continue to acknowledge them in the upcoming days for the actions they took during this difficult time."
Those honored included the operators and conductors of the MTA's R and N trains impacted by the incident, and an MTA bus driver who assisted the victims.
"Your actions are indicative of what's great about the service you deliver every day in general, and specifically the service your deliver at times of crisis," Adams said. "As a former transit police officer, I've witnessed how often you rise to the occasion during difficult times. You personify what's great about our subway system and our MTA system overall."
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Afterward, the honorees walked out of City Hall with framed proclamations and talked about what they witnessed and experienced during the terrifying ordeal.
"I thought they were just knocking on the door to find directions because they wasn't banging or anything," train operator David Artis said. "So I'm not thinking nothing's happening. But once I had to stop my train because the train was crossing in front of me, I looked out the cab door because everybody's at my cab door, that's when they told me what was going on."
Train conductor Raven Haynes wasted no time.
"My whole point was to make sure my riders were safe," Haynes said. "At no point did I think about my own personal safety. I just wanted to make sure my passengers were safe."
B37 bus driver Parla Meija also didn't hesitate, and put in long hours.
"That day, I worked from 5 in the morning until midnight," Mejia said. "Skipped my meal, and I kept buses moving."
The ceremony came as the suspected shooter, Frank R. James, remains in jail, held without bond.
He made his first appearance Thursday in Brooklyn federal court, facing federal charges after he allegedly donned a gas mask, released a smoke bomb and opened fire on a crowded subway train in Sunset Park. He did not enter a plea.
He was ordered held on a permanent order of detention, though the judge did not preclude a future bail application.
Assistant U.S. Attorney Sara Winik told the judge that the 62-year-old James, who was taken into custody Wednesday after being found wandering around the East Village and may have called police on himself, terrified the entire city.
"The defendant, terrifyingly, opened fire on passengers on a crowded subway train, interrupting their morning commute in a way this city hasn't seen in more than 20 years," she said. "The defendant's attack was premeditated, it was carefully planned, and it caused terror among the victims and our entire city. The defendant's mere presence outside federal custody presents a serious risk of danger to the community and he should be detained pending trial."
The judge agreed and denied James bail for the time being.
"The complaint speaks for itself," he said.
James' court appointed lawyer, Mia Eisner-Grynberg, agreed to his being held without bail, for now, but could seek bail later on.
New details emerged Thursday just hours after James' court appearance, in which investigators believe James may have rushed the attack he allegedly carried out, law enforcement sources told ABC News.
Investigators are working to determine whether James intended to carry out the attack as the train pulled into the 36 Street Station or whether he somehow got spooked and set off his smoke grenades sooner than intended, the sources said.
RELATED | Man who spotted subway shooting suspect Frank R. James, flagged down officers speaks out
While James made no statements to arresting officers or at the precinct, it is an avenue investigators are exploring.
As the subway car filled with smoke, it's believed James knelt on one knee to avoid the rising smoke and opened fire from that crouched position. Investigators believe that's why most of the gunshot wounds were to the legs or hands.
In a court filing ahead of his appearance, federal prosecutors called the shooting calculated and "entirely premeditated," saying that James wore a hard hat and construction worker-style jacket as a disguise and then shed them after the gunfire to avoid recognition.
Prosecutors suggested James had the means to carry out more attacks, noting that he had ammunition and other gun-related items in a Philadelphia storage unit.
While James's lengthy arrest record might seem "unremarkable," they said it paints "a picture of a person with a penchant for defying authority and who is unable or unwilling to conform his conduct to law."
Prosecutors called him a "severe and ongoing risk to the community."
RELATED | Brooklyn subway shooting heightens fears about transit safety
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