​The Port Authority of New York and New Jersey is plotting a return to its transportation roots, though unraveling its real estate tangle may be difficult.

Amid the commemorations marking the 15th anniversary of the Sept. 11 terrorist attacks, the Port Authority said it would look to sell the 104-story One World Trade Center, also known as the Freedom Tower.

Also in September, the bi-state agency announced an expanded planning process for its new bus terminal in Manhattan and plans for a $150 million bond sale for its share of the new Moynihan Station at the Penn Station site in midtown.

Port Authority in a statement acknowledged "our commitment to refocus on our core transportation mission, taking into account impacts on its financial position." A panel that New York Gov. Andrew Cuomo and New Jersey Gov. Chris Christie convened two years ago called for Port Authority to shift back to its transportation-agency roots.

The agency had intended to do that in August 2001 when it agreed to a 99-year real estate lease at the site with developer Larry Silverstein.

Six weeks later, the twin towers fell. The agency lost 84 employees that day, including executive director Neil Levin, as well as its physical headquarters.

Municipal observers and transportation experts say that beyond the tragedy, 9/11 events exposed the underbelly of a complex quasi-public agency.

"What should have gotten more attention is the impact of 9/11 on the Port Authority," said Howard Cure, the director of municipal bond research for Evercore Wealth Management. "That started to expose problems with its governance structure. There were cost overruns and delays with projects including the 9/11 memorial and the Oculus. There was a lot of political horse trading."

The Oculus, the Port Authority's World Trade Center transportation hub designed by Spanish architect Santiago Calatrava, opened several months ago at cost of $3.9 billion, about twice its original estimate. Nearly 75% of what it spent, or $2.9 billion, came from the Federal Transportation Administration as part of Washington's $20 billion aid package for the city.

"They spent the next 15 years getting back into what they shouldn't have been doing, the real estate business," said Nicole Gelinas, a senior fellow with the Manhattan Institute for Policy Research.

Moody's Investors Service rates the Port Authority Aa3, while S&P Global Ratings and Fitch Ratings each assign and AA-minus. Moody's said its rating factors in a "large and unparalleled" $27.6 billion, 10-year capital plan that focuses on financing transportation assets rather than noncore development projects.

The agency's $7.9 billion 2016 budget allocates $1.2 billion for debt service and $978 million for the new World Trade Center transportation hub. Port Authority's annual debt service has risen about 50% over the last three years.

Port Authority still has borrowing capacity, said Gelinas. "The trick is making sure you're spending it on the right projects."

The New York-New Jersey political labyrinth has long ensnared Port Authority, whose origins trace to 1920s progressive-era ideals.

"The Port Authority is one of the region's great assets. But it's become an ATM for the governors of New York and New Jersey," said Mitchell Moss, the director of New York University's Rudin Center for Transportation Policy and Management. "The board itself is highly politicized, especially so with competition between the two states getting more intense."

According to Lynne Sagalyn, a Columbia University professor and author of the book "Power at Ground Zero: Politics, Money and the Remaking of Lower Manhattan," interest-group trench warfare eclipsed idealism during the post-9/11 rebuilding.

Port Authority operations, she wrote, interweaved with real estate interests, victims' families, politicians, City Hall bureaucrats, the federal government, community groups, architectural firms and entrepreneurs, New York City Mayor Michael Bloomberg and architects Santiago Calatrava and Daniel Liebeskind, not to mention a parade of governors.

"The question, 'who's in control,' became a constant refrain," wrote Sagalyn. "The messy brawls of the past came back into play because nothing big in New York gets built without serious opposition and passionate debate, and at Ground Zero interests many and varied, public and private, swirled about seeking power and influence."

Sagalyn called out George Pataki, New York's governor at the time, for "belated, ineffective leadership" for the first five years of rebuilding, while Moss lambasted current New Jersey Gov. Chris Christie for blocking construction of a new Hudson Tunnel – the so-called Arc, or "Access to the Region's Core" project – and for his alleged role in the so-called Bridgegate scandal.

"No one has done more damage to Port Authority than Chris Christie," said Moss.

In Bridgegate, former Port Authority executive director Bill Baroni and former top Christie aide Bridget Anne Kelly are on trial in federal court over criminal conspiracy and fraud charges related to blocking traffic lanes connecting Fort Lee, N.J., to the George Washington Bridge. Prosecutors allege the move was payback for Fort Lee Mayor Mark Sokolich not endorsing Christie's re-election bid.

Stephen Eide, also a Manhattan Institute senior fellow, called for breaking up the Port Authority, saying the agency has outlived its usefulness. He compared such a move to the breakup of AT&T that wound through the federal courts in the 1970s and early 1980s.

"Now is the better time to have that discussion," he said in an interview. "We're at a point in the Port Authority's history where the perception of it has never been lower.

"There's constant haggling over the spoils, over who gets what."

Eide said any such overhaul must fully honor obligations to bondholders and identify new subsidies for unprofitable operations including the Port Authority Trans-Hudson, or PATH commuter trains.

In a letter to the Manhattan Institute's City Journal objecting to Eide's proposal, Port Authority Executive Director Patrick Foye said Eide "neglects to mention some key facts on what the agency has accomplished over the last five years."

Foye cited two major replacement bridge projects under way – raising the Bayonne Bridge to permit access for larger ships in a move to prevent losses of port business to cities such as Norfolk, Va., and the Goethals Bridge replacement, executed through the first surface transportation public-private partnership in the northeast.

"Together with a major restoration project underway at the George Washington Bridge, this is a cycle of bridge construction unprecedented since these trans-Hudson crossings were originally built in the 1920s and 1930s," Foye wrote.

Foye, whose contract the Port Authority board did not renew and who is serving until the board can find a replacement, said the agency has divested many of the "economic development" projects for which it has drawn criticism.

"They made some foolish decisions, such as the Atlantic City Airport," said NYU's Moss.

According to Foye, divestitures have included the Essex Country Resource Recovery facility and the Newark Legal Center, both in Newark, N.J., and the latter more commonly known as One Riverfront Center. Port Authority, he added, is also divesting its interest in the Bathgate industrial park in the Bronx.

While Moss does not favor breaking up the Port Authority, he said it doesn't matter who succeeds Foye as long as rough-and-tumble politics holds sway.

"It starts with the governors," he said. "They have to put good people on the board. It should not be a political playpen."

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