The LIRR said early Thursday that it had resumed its modified schedule on all branches except the Long Beach Branch after Wednesday night's delays and weather suspensions.
Customers should expect weather-related delays, longer waits and crowded cars, the railroad advised.
A roaring nor'easter battered the railroad's signal system and twice brought eastbound service to a halt Wednesday night. Just before 7 a.m. Thursday, scattered delays ranged from 11 to 33 minutes.
Just before 12:30 a.m. Thursday morning, LIRR officials said a limited schedule had resumed on all lines except the Montauk, West Hempstead and Oyster Bay branches. Customers were advised to use trains along the Ronkonkoma and Huntington routes and arrange to be picked up at the stations closest to their destinations.
The LIRR Atlantic Terminal service will remain extremely limited Thursday because of the coastal storm, and customers may wish to take a subway to Penn Station, where they can transfer to LIRR service, the railroad said.
Shortly after 11 p.m., LIRR spokesman Sam Zambuto issued a statement saying: "We will be assessing nor'easter storm damage all night."
There were power outages, downed power lines, downed trees and icing in some areas, according the statement.
Earlier Wednesday evening, all eastbound service had been twice suspended due to "weather issues," the railroad said.
The LIRR had initially suspended service systemwide around 6:30 p.m. Wednesday, citing "multiple weather-related problems," and closed Penn Station a few minutes later to additional commuters, the railroad said.
Then, about 8 p.m., the railroad announced limited eastbound service out of Penn and Atlantic Terminal. At 8:20 p.m. Penn Station reopened. But about an hour later, eastbound service was suspended again.
The railroad said the nor'easter had played havoc with the system.
LIRR customer service vice president Joe Calderone said the "primary reason" for the service suspensions was the temporary loss of the railroad's signal system "across the board, at various key locations."
"You can't run a train when you don't have a signal system," said Calderone, who added that the LIRR decided it was "safer" to keep riders at Penn Station.
Calderone said there were other weather-related problems at multiple locations, including trees down in Great Neck and Stewart Manor, a utility pole down at Little Neck with electrical wires on the tracks, and a reported third rail track fire near East Rockaway.
The storm began taking its toll on the LIRR Wednesday just as the evening commute got under way, quickly overwhelming an already fragile railroad barely recovering from superstorm Sandy.
Initially, the railroad reported "weather-related signal problems" and a downed tree across the train tracks that had forced the LIRR to suspend all service on the Port Washington branch just after 6 p.m. Wednesday. In addition, a utility pole came down on that same line, with sparking wires descending on the tracks.
There were also signal problems on the Ronkonkoma line, which reported delays of up to 72 minutes Wednesday night.
Then, shortly before 7 p.m., LIRR riders' commute was interrupted when all lines ground to halt and flashing lights on platforms said "no passengers," further frustrating Long Islanders who are still reeling from the effects of Sandy.
"This is really frustrating, especially since I've been checking the website up until just half an hour ago," said Seamus McEntee, 36, of Massapequa, a social worker who was on his way home from Manhattan when he got word of the delay in Jamaica Station. "I don't know how I'm going to get home. I would have made arrangements but it's just been a really bad week to commute."
Gary Comer, 30, was on a westbound train home to Brooklyn from his job at Broadridge Financial Service in Deer Park when the conductor announced that the LIRR was shutting down and riders had the choice of getting off the next stop, Bethpage, or staying on the train as it made local stops going back east.
"They knew this thing was coming. They shouldn't have let people get on the train," Comer said. He said it was "bananas" and "unreal" that passengers had only a few minutes to decide whether to get off the train.
Passengers tweeted about evening commutes that took as long as five hours of waiting and riding. Once the system started up, one of the biggest delays was the eastbound train due in Babylon at 7:27 p.m. -- it was going to be 108 minutes late, LIRR tweeted just after 8:30 p.m.
Calderone said LIRR officials were frustrated: "We definitely could have done without this one. That's for sure," said Calderone. "We're still recovering from the superstorm. Our infrastructure is certainly fragile. . . . This is an insult-to-injury kind of thing," he said.
Nassau's NICE Bus system also had told customers to expect the new storm to have an impact on service.
"Customers should plan for the possibility of a longer commute depending on conditions," NICE spokesman Andrew Kraus said Tuesday.
"The events of the previous days have obviously given NICE an idea of what areas might be more vulnerable. NICE's goal is to continue to provide normal service, which obviously can change depending on conditions or forecasts."
Meanwhile, the LIRR continued its gradual climb back from Sandy Wednesday morning, as it extended service to Montauk. It also introduced bus service between Lynbrook and Island Park to accommodate customers on the particularly devastated Long Beach branch -- the only LIRR line still without any train service. The buses will leave every five minutes during peak hours and serve all local stops along the line.
"Thank God," Laura Tyson, 57, of East Rockaway, said upon learning about the bus service Wednesday. Tyson, a special education middle school teacher in Brooklyn, said it's been difficult to get to work since Sandy because of the lack of transportation options.
On Tuesday Tyson took a cab to Lynbrook station, only to find crowds so thick she was unable to board a train.
"When I finally got there it was so packed that you could not get on. . . . I could not do it," said Tyson, who was excited about the LIRR adding the connecting bus service. "I'm definitely going to do that tomorrow morning."
With two of the four East River rail tunnels service at Penn Station still out of service, the LIRR continues to operate far fewer trains than usual. That's resulted in major crowding on trains and at stations.
The LIRR continued to ask customers to consider staggering their work hours so that they are not traveling at peak times. They have also issued alerts to remind customers of train etiquette.
"When boarding LIRR trains, please move inside and proceed towards the middle of the car, so others behind you have room to enter safely. Please do not block train aisles or doorways," the LIRR told customers in an email with the subject line "courtesy matters."
The LIRR continued to charge off-peak fares on all trains and waive onboard purchase fees. Long Beach branch tickets are being honored on all lines. And the LIRR has opened its Long Beach station waiting room as a "comfort station" for community residents during daytime hours.
The LIRR has also worked with municipalities to waive resident parking restrictions at several stations, including Lynbrook and Rockville Centre.
The Metropolitan Transportation Authority also continues to make progress on its New York City subway lines. The MTA announced Wednesday morning that it had restored some service on the G line between Brooklyn and Queens. On Tuesday, service was restored on the A line in upper Manhattan.
"We are working day and night to restore service as quickly as possible to give customers more travel options after the storm each day," MTA chairman Joseph Lhota said. "We will continue to add service incrementally, only when it is absolutely safe to do so and doesn't overcharge the system. Given the strain on the system, we still encourage our customers to allow extra time for their commutes."
The Queens Midtown Tunnel remains open only for buses.
The MTA has postponed a planned public hearing scheduled for Wednesday night at Farmingdale State College regarding its proposed 2013 fare and toll increases.
A new date has not been set, but MTA spokesman Kevin Ortiz said the agency is going ahead with plans for "video conference hearings" next week at two key LIRR stations.
On Nov. 13 at Hicksville and Nov. 14 at Ronkonkoma, morning commuters will be able to record their testimony on video cameras set up inside station buildings. Those videos will be reviewed by the MTA board before it votes on Dec. 19 whether to raise fares.
With Candice Ferrette, Patricia Kitchen and Ellen Yan