It took seven months for A train service to resume in the Rockaways.
Meanwhile the R train is still not running between Brooklyn and Manhattan.
The MTA learned lessons before and after the storm.
Here's what the MTA got right during Sandy. First, it shut the system down early giving plenty of time to move all the subway cars and commuter rail cars to high ground. And as the last trains left the tunnels, workers took another precaution:
"Remove sensitive electrical gear and signals and switches and so forth," said Bob Yaro of the Regional Plan Association. "The stuff had been mapped ahead of time. The last trains that went through the tunnels before they shut the system down actually removed a lot of that sensitive equipment which would be very very difficult to replace."
That helped get nearly 80-percent of the subway up and running four days after a storm that caused billions in damage to the system:
"My sense is they got a tremendous amount of this right. The fact the rolling stock was all safe. They didn't lose anything. The ability to get the system back up and running again was really quite remarkable," said Yaro.
But where some say the MTA failed is in protecting its tunnels and subway stations. The most vulnerable in lower Manhattan, South Ferry Station and White Hall protected against a predicted 11-foot surge by plywood and a couple of rows of sandbags.
"The kinds of barriers they put up, plywood, the minimal stuff could have never stopped a disaster the kind we predicted and told them about. It was malfeasance of the highest order," said Richard Brodsky of NYU Wagner School.
In 2006, Richard Brodsky chaired a legislative committee that warned the MTA that the "CITY IS DUE FOR A MAJOR HURRICANE" that "WILL CAUSE OVERWHELMING FLOODING". Brodsky says the MTA failed to meet its responsibility under New York State Law to minimize the effects of disasters like Sandy by better protecting the tunnels, including the Brooklyn Battery and Queens Mid-Town Tunnels which had NO flood protection and suffered damage that kept them closed for days:
"In this case, the failure to sandbag these tunnels remains a major and expensive and damaging failure by the MTA," said Brodsky.
"The reality is we sealed up with wood and apoxy as much as we possibly could," said Joe Lhota, the head of the MTA during Sandy.
He defended the agency's storm preparation insisting the record surge overwhelmed their robust efforts.
"Do I have to get the pictures for you to get the number of sandbags to seal up?", said Lhota. "We had a water surge like we never had before in lower Manhattan.
"The sandbag height was only two or three feet at some of these subway tunnels, the surge was 14 feet," Eyewitness News said to Lhota. "Okay, next time they'll do a better job, no one had ever seen a surge like this before," he responded.
The MTA says it currently has 50 projects in the design phase, and eight projects already under construction, all of them geared to protect subway tunnels and stations from future coastal storms.
Researchers from West Virginia University are working on a possible flooding safeguard: an inflatable tunnel plug. It could be used to prevent flooding in subways and tunnels. However, it's still years away from becoming a reality.
If you have a tip about this or any other issue you'd like investigated, please give our tipline a call at 877-TIP-NEWS. You may also e-mail us at email@example.com.