Governor Spitzer and Mayor Bloomberg are facing growing unrest over the decrepit state of the city’s transit infrastructure, after almost every subway line was brought to a standstill yesterday morning by a thunderstorm and tornado that dumped 3 inches of rain onto the city and overwhelmed the drainage system in minutes.

It was the third time in seven months that heavy rain temporarily paralyzed the city’s subway system. Once again, the collapse of the system was accompanied by a communication breakdown that left New Yorkers in the dark about which stations were shut down and which alternative routes to take. Even the Web site of the Metropolitan Transportation Authority was down after being inundated by customers seeking help.

In what is becoming a disturbing routine that raises questions about the city’s ability to react to weather, much less a large-scale disaster, thousands of commuting New Yorkers were forced to trek in the stifling heat or claw their way into overcrowded buses to get to work during the morning rush hour.

“It’s frustrating. It’s insanity,” a 45-year-old woman making her way toward Midtown from the Upper East Side by bus, Hope Kotler, said.
Acting by turns defensive and exasperated, Messrs. Bloomberg and Spitzer, who had assured New Yorkers that city and state agencies had taken steps to guard against weather-related breakdowns, said the city was taken by surprise by the ferocity of the storm and the most severe tornado to touch down in Brooklyn in half a century.

“I don’t know that God has rush hour in mind when storms hit,” Mr. Bloomberg said at a press conference.

Bay Ridge, in Brooklyn, bore the brunt of the destruction from the tornado, which uprooted trees, tore open the roofs of several brick row houses, and devastated a car dealership with winds of 135 mph. One woman in Staten Island was struck and killed yesterday morning on a highway when she exited her car after getting stuck in an underpass. The storm caused delays at all three regional airports.

Mr. Spitzer ordered the executive director of the MTA, Elliot Sander, to conduct a 30-day review to figure out how the transit system can better cope with heavy rain. The governor said the chronic problems with the system would not deter his administration from expanding and building new subway lines.

“We are not going to pull back in any way, shape, or form from our dedication to expanding the system,” Mr. Spitzer said.

Mr. Sander, who was appointed by Mr. Spitzer, pinned much of the blame on official forecasters, whom he said gave little warning about the storm until it was too late to make critical preparations, such as covering vents with plywood and sandbags.

“The timing and intensity of the storm took us by surprise because it was not predicted by the National Weather Service,” Mr. Sander said at a press conference yesterday in Mr. Spitzer’s Manhattan headquarters.

He said he shared the “frustration” of New York commuters. “I take the system basically daily and so I certainly appreciate it. The fact is we have a 100-year-old system, and that is a constraint. We may be dealing with meteorological conditions that are unprecedented. It certainly looks that way in the last seven months.”

A spokesman for the National Weather Service, Michael Trajbar, said the agency issued a tornado warning and a flash flood warning for all five boroughs at 6:08 a.m. The tornado touched down at about 6:30 a.m. Mr. Spitzer said he might consider building an alternative weather predicting forecast service inside the MTA.

By evening, the majority of the subway system’s 23 lines were operating. Major portions of the F (between Long Island City and Jamaica), G (between Long Island City and Bedford in northern Brooklyn), and V (between Second Avenue and Forest Hills Queens) lines were out of service. Service along the Queens Boulevard corridor was slowly resuming service.

About 17,000 customers through all five boroughs and Westchester County were without power just before sunrise, a Consolidated Edison spokesman said. By mid-afternoon, power had been restored to about 15,000 customers.

Many city leaders directed angry remarks at the MTA.

“Rain is not a rare occurrence in this city,” the speaker of the City Council, Christine Quinn, wrote in a letter yesterday to the chairman of the MTA, Peter Kalikow.

Council Member John Liu, who heads the transportation committee, questioned how the MTA would handle a more serious emergency if the system can be grounded by a single hour of hard rain. “With proper planning and management, the huge crush of commuters waiting for hours on platforms or in train cars could have been dramatically reduced,” he said in a statement.

The president of Manhattan, Scott Stringer, criticized the MTA for failing to alert its station employees about the status of trains. “Information breakdowns are inexcusable and must not be repeated,” Mr. Stringer said in a statement.

Mr. Spitzer defended Mr. Sander, saying the MTA chief has “made a remarkable effort … to increase the flow of information to the public.”

Morning commuters, meanwhile, said they hadn’t suffered such an infuriating trip to work since the transit strike in December 2005.

His navy blue collared shirt dark with sweat, Kevin Smith, a research assistant at Standard & Poor’s, arrived on Wall Street four hours after he left his home in Left Pawnik, N.J.

Yesterday morning, he boarded a bus to the Port Authority Bus Terminal, transferred to a crosstown bus to Madison Square Park, boarded a subway to Canal Street, and then walked to work.

“Maybe the MTA needs a contingency plan,” Mr. Smith, 22, said after stopping at the Gap to purchase a new shirt before heading in to work.

Jerry Vaca, 35, who lives in the Bronx and works as a doorman on 43rd Street, said his 35-minute commute to work this morning took over three hours. “It felt like September 11, walking back,” he said. “There were no cabs, and people were fighting for the buses.”

The flooding problems arise when a large volume of water enters the system through grates and subway entrances in a short period of time. When the city’s drainage system is unable to absorb any more water, it reenters the subway system as fast as the equipment can pump it out. “Our pumps are working, but it’s like a dog chasing its tail,” a transit authority spokesman, Paul Fleuranges, said. If water is approaching the third rail, the MTA cannot run service.

Once the water is pumped out, transit workers must clean up what’s been wash in and make sure circuits and switches are functioning properly before service can resume.

The Transit Authority has spent $357 million since 1992 to rehabilitate 269 pump rooms. Another $115 million has been earmarked for pump upgrades to be completed in 2010, and transit advocates have urged the MTA to work at a faster place improving its pumps.

In the 1980s and the 1990s, “the system was never shut down due to rain,” the chief attorney of the Straphangers Campaign, Gene Russianoff, said. The system-wide meltdowns began in late August of 1999, and then hit again in September 2004.

“It’s fair to say it’s an act of God, but they’re not unpredictable anymore,” Mr. Russianoff said. “This is going to happen with regularity,” he said, blaming climate change.

A 2004 report by the MTA’s inspector general found “historic neglect” of valves that are designed to prevent city sewers from backing up into subway tunnels. There were no records of the valves being inspected for decades. First responders to the floods sometimes took over an hour to arrive at the scene, and sometimes never showed up at all. Mr. Sander said the MTA has implemented the report’s recommendations.

“The city’s sewer system is not equipped to handle major storms,” an MTA board member, Andrew Albert, said. “Like the horrible breaching of the levies, you’ve got to do things to prepare in the future.”