While Hurricane (now tropical storm) Irene wrecked havoc along the East Coast, the effect was not as bad as anticipated in New York City, where all transit service had been stopped on Saturday afternoon in preparation for the hurricane that hit later that day.
"Several subway train yards were flooded on Sunday afternoon, and workers were trying to pump out water so that trains could run on their proper routes. But there were minimal signs of damage to the overall system, officials said, and the underwater tunnels that were considered vulnerable to the storm were mostly untouched.
Many trains had been removed from low-lying yards in advance of the storm, which made it easier for workers to restore them to service for Monday."
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Irene update on NY/NJ commuter rail & subway service restoration
Just to clarify, per the NYT: New York Subway Running in Time for Morning Commute: "The Metro-North Railroad said that it would operate no trains at all on Monday on all three of its lines, which serve areas of New York and Connecticut. Its tracks sustained extensive damage from flooding, fallen trees, and mudslides."
However, LIRR fared much better: "The Long Island Rail Road said that it is “operating near-normal service this morning on six of its branches,” but with service suspended to certain stops."
Per WSJ: Commuters in Line for Long Rides
Restarting the City's Transit System Proves to Be a Complicated Process: "Metro-North Railroad and New Jersey Transit were going to remain almost completely shut down. Between the two railroads, only a small New Jersey Transit branch to Atlantic City would run."
Furthermore, the WSJ article explains what was necessary to restore the subway service that was damaged by the hurricane: "To bring the subways back on line, workers had to pump out floodwaters pooled on tracks and remove any debris. They took dried out soggy signals. Once the tracks were clear, drivers had to return about 2,000 subway cars to their terminals. Then, they needed to conduct test runs on all of the tracks."
[See Gothamist: MTA Offers Photographs Of Irene-Wrecked Stations, Tracks]
And, as for who called for the shut-down of MTA, a state agency, "Mayor Michael Bloomberg defended the decision by Gov. Andrew Cuomo to shut down MTA service, saying the storm might have done longer-term damage to transit equipment had cars not been evacuated from flooded yards."
Irvin Dawid, Palo Alto, CA