As Hurricane Sandy raged on Monday night, Joseph J. Lhota, chairman of the Metropolitan Transportation Authority, found himself on the familiar territory of Ground Zero.

In 2001, as a deputy mayor in the Rudolph Giuliani administration, Lhota had rushed to the same place, watching as one of the World Trade Center towers fell to the earth. Eleven years later, he returned as a new catastrophe was unfolding, in what seemed like some kind of a twisted echo: floodwaters were pouring into the construction site where the towers once stood.

“It’s hard not to notice that this is again happening in the same little patch of Lower Manhattan that was so challenging for him 11 years ago,” said Adam Lisberg, the MTA’s chief spokesman. “He certainly noticed the confluence.”

MTA chief Joseph Lhota, center right, served as deputy mayor to Rudolph Giuliani and played a crucial role in 9/11 recovery. Here Lhota bids farewell at the end of 2001. AP Photo/Beth A. Kaiser

As the MTA’s chairman, Lhota now confronts one of the most daunting challenges in the wake of Hurricane Sandy: getting the region’s subways, trains, and buses up and running again.

The task is formidable: the Authority’s tunnels flooded, its storage facilities were damaged, and one of its Manhattan stations was filled to the ceiling with water. A large motorboat perched high and dry next to commuter rail tracks in Westchester County.

But Lhota’s former colleagues say that the man charged with cleaning up the mess is uniquely qualified for the job.

After working as deputy mayor for operations in the months following 9/11, Lhota is “battle tested,” according to Sunny Mindel, a former Giuliani spokeswoman. And as a former budget director and finance commissioner, he knows the ins and outs of city government as well as anyone else.

“If there’s anyone up to the task, it’s Joe Lhota,” said Randy Mastro, who worked with Lhota in the Giuliani administration and was his predecessor as deputy mayor for operations. “He’s the right man at the right time at the MTA.”

Joseph Lhota at his state Senate confirmation as MTA chairman earlier this year. AP Photo/Mike Groll

Working under a famously confrontational mayor, Lhota was the man Giuliani relied upon to negotiate some of the administration’s thorniest political problems, by whatever means necessary. In interviews, Lhota’s former colleagues describe him as a straightforward, practical manager who tackles problems head-on.

Even those on the other side of the negotiating table praised Lhota’s no-nonsense style, which helped to broker a compromise in a long-running dispute between Giuliani and a city councilman, Stephen DiBrienza, in the late 1990s.

The feud, over the city’s policies affecting the homeless, was once described by the Times as a “dispiriting political vendetta.”

But when it came time for détente, there was one official from the Giuliani administration that DiBrienza could reason with: Lhota, who at the time was deputy mayor for operations.

“He was kind of an exception,” DiBrienza said. “He was the one guy who actually worked hard at trying to resolve whatever final differences we had…. He was tough, but he was detailed and logical.”

The 58-year-old son of an NYPD police lieutenant, Lhota was born in the Bronx and raised on Long Island before earning degrees from Georgetown and Harvard. He spent 15 years as an investment banker before joining the Giuliani administration.

In his work overseeing the city budget, Lhota fostered a collegial environment with other Giuliani officials, according to John Dyson, another deputy mayor who hired Lhota into the administration as his chief of staff in 1994.

In order to extract cuts from city commissioners who typically “defend every single thing to the death,” Dyson said, Lhota and Giuliani instituted a new budgeting system designed to encourage cooperation.

Rather than automatically imposing cuts from the top down, the pair told commissioners that if they could come up with their own plans to reduce costs, their departments could keep some of the savings.

“There was a carrot and a stick in the idea,” Dyson said. “It changes the psychology completely.”

As deputy mayor for operations, Lhota oversaw the day-to-day grind of city government, from the police and fire departments to sanitation, said Mindel, the former Giuliani spokeswoman.

“He was the one who made sure the garbage got picked up,” she said.

But it wasn’t just trash; Lhota was also tapped by Giuliani to guide the administration through several controversies, like the standoff between the mayor and DiBrienza.

Lhota’s direct manner has sometimes flirted the line with bullying, most famously in an episode where he called Wall Street firms that did business with the Giuliani administration and urged them to boycott a fundraiser for a nonprofit watchdog group, the Citizens Budget Commission, that had drawn the mayor’s ire.

But with DiBrienza, that wasn’t the case. The councilman had advocated a policy to scale down the size of city homeless shelters; Giuliani responded by trying to site a new one in DiBrienza’s district by evicting a senior center and child care facility.

“It became this personal attack that lasted for months and months and months,” DiBrienza said. “At the end of the cycle, it was Joe Lhota who said: ‘Listen, can we meet?’… There were one or two areas where we saw room to negotiate. His requests were not unreasonable. It was substantive, and we got it done.”

That substantive style has extended to his work at the MTA, where his experience in the nuts-and-bolts of city government has helped fill in gaps in his specific knowledge about subway systems and commuter rail.

“While he’d be the first to admit that he wasn’t a ‘train guy’ when he came in last year, he’s a hell of a manager,” said Lisberg. “If you can be a successful deputy mayor for operations in New York City, you can run anything in the world.”

Lhota’s biggest challenge during his Giuliani years — and perhaps the best indicator of how he will respond to Sandy — was the September 11 attacks.

Just before 9 a.m that day, he was at his desk scrawling a note to a secretary when he heard an explosion, ran outside, and saw one of the Twin Towers in flames.

After driving to the scene and surviving the buildings’ collapse, Lhota set up camp with the rest of Giuliani’s staff in a pier on the West Side.

Mindel recalled how in the days after the disaster, Lhota would systemically gather information about the recovery effort — from the tonnage of debris removed from Ground Zero to the number of ambulance pickups — and present it to staff.

“He had categories, and a couple times a day he would fill us in,” she said. “He knows how to present statistics and important, critical information in a way that is comprehensible to the listener.”

That skill, Mindell added, will be important in the days ahead, as the MTA labors to get the subways up and running after Sandy.

“New Yorkers are very good if they have proper information,” she said. “They’re not very good if they don’t get accurate information.”

After leaving the Giuliani administration at the end of 2001, Lhota spent about a decade in the private sector, working for as an executive for Cablevision and The Madison Square Garden Company.

Governor Andrew Cuomo appointed him to the helm of the MTA a year ago, and in that position — typically a thankless one that’s quick to draw venomous tabloid editorials–Lhota has made the most ripples not with service cuts or fare hikes (though one is currently in the works), but with his colorful Twitter feed, and with one outburst at an Authority board member.

He spent the hurricane delivering briefings with Cuomo, and reviewing damage to the city’s transit system.

Between site visits, Lhota has been holed up with his emergency response team at the MTA’s headquarters on Madison Ave., and has gotten “a few hours of sleep,” Lisberg said.

Mastro, Lhota’s predecessor as deputy mayor for operations, said that the MTA chairman is likely “asking a lot of tough questions,” and looking at all the available strategies to restore service.

“He’s not a one-move chess player,” Mastro said. “He’s a think-several-moves-ahead kind of guy.”

Dyson said that Lhota’s experiences make him just the man for the job–even if dealing with two unprecedented crises in just over a decade is an unenviable task.

“I’m very glad he’s doing it, although I’m sure it’s no fun,” Dyson said. “It’s a good thing he had a few years off in between.”