The transit mayhem came as an icy winter storm bore down on the city, dumping more than a tenth of an inch of ice on Queens, according to the National Weather Service.
The delays also came as a manhole exploded in Brooklyn, hitting a man in the head with a cover.
Earlier in the morning, an umbrella caught fire on the third rail at 52nd Street, disrupting service, the MTA said. Officials at the Office of Emergency Management said that the ice accumulated while trains were stopped as crews cleared the umbrella.
But the MTA said the events were "unrelated" because they were in different locations in different times.
Trains were suspended between 42nd Street and Flushing-Main Street after a Manhattan-bound train stalled just north of the plaza because of the ice build-up about 9 a.m., an MTA spokeswoman said.
The Long Island Rail Road was also cross-honoring fares at Flushing, Mets Willets Point, Woodside and Hunters Point, the MTA said.
And shuttle buses were running between Queensboro Plaza and Flushing-Main Street in both directions. Massive crowds lined up for the buses in both places.
Most trains were brought back to nearby stations to let passengers off, but there were four trains on express tracks between stations that had to be evacuated, the spokeswoman said.
All trains were unloaded as of 11:30 a.m., according to the MTA.
Monday afternoon, the MTA was testing out the rails in an attempt to bring trains back online, but there was no timeline for service restoration. Some stations, such as Flushing, were roped off with police tape. Turnstiles were disabled at others.
The mayor's office referred questions to the MTA. The governor's office, which shuttered the subway system ahead of the expected blizzard last week, did not respond to a request for comment.
Ashley Carr, 30, said that her 6-stop commute between 52nd Street and Hunters Point Avenue took her a whopping three hours to complete.
She initially got on a train at 52nd Street, but had to get off at 46th Street because trains were not running local to Manhattan. From there, she had to go back to Woodside and board an express train towards Manhattan. But that train got stuck near 33rd Street.
"We heard everything from mechanical issues to 'there's something on the track' to a stalled train," she said.
Despite the delays, she said that most people onboard were frustrated but not freaking out.
"Some people were making jokes about it and how ridiculous it is," she said. "For the most part everybody was in moderately decent spirits."
At 52nd Street in Woodside, dozens of passengers waited in the freezing rain to find alternate transportation to their destinations, waiting as packed Q32 buses went by.
Bryan Nunez, 19, said he had boarded a Manhattan-bound 7 train around 9:45 at 82nd Street to head to class at Baruch.
The train moved slowly at first but stopped for good at 52nd Street in Woodside.
"They made us walk up on the cars," he said. "The trains weren't going to Main Street or 82nd Street."
Other passengers were still trying to get into the station even after the trains were evacuated.
"Five or six Q32s have come by and been full," said Helen Gutowski, 24. "Cabs have been full."
Trains were brought back into the station at 61st Street-Woodside instead of continuing on to Manhattan.
One rider who got on at Woodside enroute to Manhattan said the train had gotten near Queensboro Plaza before it was towed back to Woodside, a process that took a half-hour.
"They kept apologizing. They were very nice," said the straphanger, who gave only her first name, Krystal. "I totally understand, so it's not like I'm mad or anything. At least we are above ground so I can email."
The MTA chose not to alter regular subway service for the winter storm that was set to pummel the city with freezing rain and icy conditions, instead opting to deploy extra crews and gear.
"[The MTA will deploy] snow and ice-fighting equipment across the rail network to operate overnight to keep rails free of snow," the MTA said Sunday.
"Extra crews have been scheduled to keep platforms and stairs free of snow and ice, and chains are being placed on NYC Transit and MTA Bus equipment for added traction," the transit authority said.
The spokeswoman did not have an estimate for when regular service would resume.
Riders should check the MTA website for updates.
Additional reporting by Jeff Mays.