The "Bridgegate" scandal that rocked New Jersey Governor Chris Christie's administration earlier this year is threatening a deal that would allow developer Larry Silverstein to finish building the next World Trade Center skyscraper. Silverstein needs a guarantee from the Port Authority of New York and New Jersey to secure a $1.2 billion construction loan for 3 World Trade Center. On Wednesday, the agency's board will vote on whether to approve that guarantee, part of a deal that would provide hundreds of millions of dollars more to the Port Authority and allow it to foreclose on the $2.4 billion tower if Silverstein cannot pay debt service costs. But Silverstein's deal, even with the concessions to the Port Authority, has become entangled in a fierce debate within the agency over its mission, including whether it should be in the real estate business at all. Read More Chris Christie's lawyer clears governor of 'Bridgegate' Those questions have emerged since the so-called Bridgegate scandal erupted earlier this year. Operatives loyal to Christie's administration caused massive traffic jams on the George Washington Bridge in September, an alleged act of political retribution against a local New Jersey mayor who did not endorse Christie for reelection.

One World Trade Center and the World Trade Center Transportation Hub under construction, March 11, 2014 in New York. Stan Honda | AFP | Getty Images

The controversy has led to scrutiny of every corner of Port Authority operations, as well as the resignation of the agency's deputy executive director and board chairman, both Christie appointees. Most pertinent to Silverstein, it has also led to open debate at the authority—something in which it has not frequently engaged—and to the creation of an internal oversight committee examining operations, governance and political meddling. Critics have charged that rebuilding the World Trade Center area, which stalled for years after the September 11, 2001 terrorist attacks decimated the site, has taken too much time and energy away from other projects that are more critical to its bi-state transportation mission. Read More Another headache for New Jersey's Christie: Class-actin suits

The rebuilding of the World Trade Center "opened the door" for an expansion into areas outside the agency's mission, said Robert Yaro, president of the Regional Plan Association. While the RPA was originally in favor of the authority leasing the site, the association had also hoped the Port Authority would sell the land, he said on Monday during a meeting of the Port Authority's new oversight committee. "The only thing to do now is to finish the project," he said, adding that the agency should then get out of all other extraneous projects. Port Authority commissioner Kenneth Lipper has lobbied openly and repeatedly against the Silverstein loan guarantee. Acting Board Chairman Scott Rechler has said he supports it, however.