“This is a logical place for people to invest homeland dollars,” said James Dyer, a Washington, D.C.-based lobbyist who is representing Vornado Realty Trust and the Related Companies, the two firms that formed a joint venture to redevelop the Farley Post Office into Moynihan Station. “Anytime you have a station carrying more people through it that go through the airports at any one time, you obviously are going to have security concerns.”

The developers paid Mr. Dyer’s firm, Clark & Weinstock, $220,000 in the first half of the year to lobby the Department of Homeland Security as well as other more obvious targets, such as Amtrak and the Department of Transportation, according to federal lobbying records.

The $865 million proposed conversion of the Farley Post Office, at 33rd Street and Eighth Avenue, into a train station had been fully funded when the Pataki administration approved it last year. But that proposal was never finalized because the developers proposed a far broader, and expensive, plan that involves moving Madison Square Garden and redoing Penn Station underneath.

The new Penn Station, dubbed Moynihan East, could cost as much as $2 billion, according to rough estimates. In addition to the $450 million that the developers have reportedly committed, the state is expected to contribute more and also seek funds from the city and the federal government, including the Homeland Security Department. The fund amounts aren’t yet clear.

“We do believe that we can make the case that federal transportation funding, homeland security funding and historic preservation tax credits are all appropriate sources of funding for this project,” Patrick J. Foye, the co-chairman of the Empire State Development Corporation, said. “I think with 550,000 New York and New Jersey residents going through this facility every day as a key regional and national transportation hub, that it would be entirely appropriate for the federal government to contribute homeland security funds.”

Tom Schatz, the president of Citizens Against Government Waste, a private nonpartisan watchdog organization based in Washington, said that the lobbying activity at the federal level indicates that the developers are seeking special earmarks for the project. The Homeland Security Department gives to few of these so-called pork projects, he said, distributing its money instead in lump sums to states and cities to divvy up, or to particular types of security operations, such as screening cargo that arrives by ship.

Mr. Schatz said that it would distort the purpose of homeland security funding if money was used to build a new train station.

“After the facility is completed, there might be some money available for security operations,” he said. “But if [the] Homeland Security [Department] becomes a builder and starts supporting construction, almost anything can be built with homeland security money. That is a big concern because that takes money away from causes that are more crucial for protecting homeland security, such as protecting the ports, protecting the borders, screening passengers in airports.”

Somehow, months or even years later, Harlem, or at least a vocal portion of it, is still not convinced. At a Dec. 12 City Council hearing, Mr. Bollinger drew a groan from the audience when he posited that there existed “a sense that we have established trust between Columbia University and the surrounding neighborhood”—a groan that was loud enough to draw gaveling and an admonishment from the City Council member chairing the meeting.

The opposition may not matter in the end: The City Council was expected to ratify on Dec. 19 or, at the latest, by mid-January, with just a few symbolic "nay" votes, the rezoning that would make the 17-acre campus in West Harlem possible.

But why, if the university spent all this time—not to mention money—trying to reach out to Harlem, do so many people feel that Columbia has not been listening?

Early on, Mr. Bollinger spoke of the need to overcome the town-gown tensions of the past, and several instruments were set up to forge a cooperative relationship. Community advisory meetings were held and a turning point in the relationship was promised.

“I think now I was incredibly naïve in thinking that we could work together on this,” said Jordi Reyes-Montblanc, the chairman of the local community board. “They did nothing to actually change their plan when we raised objections to it.”

A pastor of a West Harlem church on the edge of the expansion zone, the Rev. Earl Kooperkamp of St. Mary’s Episcopal, was more moderate in his appraisal, though nonetheless skeptical.

“Columbia has resources and a good vision, and that’s a good thing,” he said. “But all too often there has been a dialogue to the deaf. I’m not sure Columbia has been hearing it.”

To some extent, any plan to build seven million square feet of anything anywhere would run into resistance. The transformation of the proposed site—most of it between Broadway and 12th Avenue from 125th to 133rd streets—would be total. A low-slung manufacturing area with dissolving sidewalks is about to be turned into a new-fangled campus with gleaming 25-story buildings. Just two or three historic buildings are to be preserved under Columbia’s plan. The current residents would be moved, somehow with their consent.

From Columbia’s perspective, the move would be historic, comparable to the decision to move to Morningside Heights over 100 years ago. The new campus would address a severe space deficit that Columbia says it suffers compared to other top schools, and add enough floor area to grow for another 30 years.

But in this case, Columbia’s history with the community, the nature of the opposition it faced and the awkwardness with which it stated its case conspired to make the expansion a particularly difficult sell.

It was clear from public hearings that the memory of the university’s attempt to build a gym in Morningside Park lives on strongly, even though it happened almost 40 years ago. “Don’t trust Columbia University,” Councilman Charles Barron, an East New York Democrat, proclaimed at last week’s City Council meeting. “History has shown that they cannot be trusted.”

On top of that, Harlem’s well-organized tenants groups, already upset about gentrification that it could not control, saw in Columbia an enemy it could recognize and fight. They launched a no-holds-barred assault on the plan, booing Mr. Bollinger, and even former Mayor David Dinkins, a Columbia professor, when they spoke in support of the expansion at a public hearing in August.

The opposition may have turned off political leaders, but it energized its base with a clear message: Columbia was an outsider eating up Harlem. The university tried to defuse this argument by pledging that it would not seek to use eminent domain to displace residents, only businesses. Yet the distinction was publicized only late in the game, and it did not do anything to temper the objections of two commercial property owners who did not want to sell to Columbia. One, Nick Sprayregen, hired a lawyer and publicist to fight it. The other, Anne Whitman, supported an opposition group, the Coalition to Preserve Community, by contributing money to pay for photocopies and the like, according to Tom DeMott, a founder of the CPC.

Columbia, on the other hand, seemed to be spreading several messages. One was that it was misunderstood. Mr. Bollinger, for instance, told The Observer in January that the relationship with Harlem was “quite positive, much better than it was, and not as appreciated as it ought to be.” He went so far as to say about surrounding residents, “Their lives will be very significantly improved by Columbia’s presence. If I didn’t believe that, I would not have reached the decision to go there.”

Meanwhile, other officials and university brochures tried to play up how much the school already was doing for Harlem by advertising its community health services, a legal aid clinic and the fact that 30 percent of its workforce lived in Upper Manhattan. They trumpeted a “Columbia-assisted” public high school that would be located on the new campus—although, the university’s senior executive vice president, Robert Kasdin, said last week that Columbia is not paying for the construction of the school, just the property on which it will stand.

At the same time, when Columbia tried to work with Harlem, that cooperation occasionally bit back. The school incorporated suggestions it heard from a series of public meetings four years ago into the design of the expansion: ground-floor retail, an absence of gates, and green space, all intended to open up the proposed campus in a way that the current 116th Street one is not. Yet those elements were almost taken for granted by the time the proposal made the rounds of the community board.

What is more, Columbia agreed early on to negotiate a “community benefits agreement” under which the university would promise job-training programs and support for affordable housing. But in pledging to negotiate with only one organization that claimed to represent the community, it had little choice but to shut down discussions with others—one of whom, the Rev. Calvin O. Butts III, the prominent pastor of Abyssinian Baptist Church, complained publicly about the shut-down on cable television. (At the same time, however, Columbia went ahead with separate negotiations with Manhattan Borough President Scott M. Stringer when it was his turn to weigh in on the proposal. He endorsed it.)

Perhaps the biggest complaint among dissenters was Columbia’s reaction to the local community board’s 32-2 vote against the expansion in August. The board attached 10 conditions that it wanted changed, ranging from forswearing eminent domain to a higher standard of environmental design than what the university has committed to. While Columbia has made a few gestures to address a couple of these items—such as building more than 800 apartments on the new campus to house university affiliates—it has so far stayed silent on others, such as landmarking historic buildings in the footprint.

“I think Columbia was probably even more arrogant than Forest City Ratner,” said Ron Shiffman, a Pratt Institute professor who acted as a consultant to the community board, referring to the developer of Atlantic Yards in Brooklyn. “They completely disregarded all of the modifications that the community board suggested.”

Last week, Columbia took a potentially huge step to reduce the need for eminent domain when it began negotiating with Mr. Sprayregen, owner of Tuck-It-Away Self-Storage, to trade properties instead of seizing them. But it remains to be seen whether those negotiations continue after the City Council vote, or were merely a way to look cooperative.

THE UNIVERSITY SEEMED to make it easier for those opposed to it by rolling out its plans early; taking a long time to get its paperwork finished; and only belatedly lining up supporters who would be willing to take to the mike at public hearings. It hired former David Dinkins aide Bill Lynch as far back as last December to form a coalition, although it took until this August for the group to go public. The Coalition for the Future of Manhattanville now lists 20 groups or individuals, some of them quite prominent—like Hazel Dukes, the president of the New York State conference of the N.A.A.C.P.—yet the very manufactured characteristic of this coalition has given die-hard opponents another reason to grumble.

La-Verna Fountain, a Columbia spokeswoman, questions the depth of the community opposition.

“I think it is interesting that when people say ‘community,’ they paint it with very broad strokes,” she told The Observer. “There are certainly very strong, viable voices that are very much in support of this.”

Certainly, among the strongest voices are the ones who are voting and making decisions on this matter. No matter how hard Columbia found it to convert certain elements of the community, it reached out early to the most prominent elected officials and won their support, among them Mayor Michael Bloomberg and Congressman Charles Rangel. City Council members were attracted to the promise of 6,000 new jobs and a substantial contribution to an affordable housing fund.

But Columbia wasn’t able to convince everybody.

The agreement, according to a source familiar with the negotiations, is all set except for one crucial element: the numbers were left blank. The source said that the group, the West Harlem Local Development Corporation, has gone into these negotiations asking for a total of $247 million in benefits. Columbia has not offered much more than the $32.5 million pact it made with Manhattan Borough President Scott M. Stringer in September, according to the source.

One new element that apparently both sides agree on: a public laboratory school, for pre-K through 8^th grade, that would be affiliated with Teachers College, which is separate from, yet related to, Columbia, and supported by the university. This would come in addition to the high school for which Columbia will donate land that has already opened in temporary space.

Oh, and one other thing: the name has changed from a “community benefits agreement” to a “community partnership agreement.”

“Nobody is concerned that a real parking issue is going to develope between 60^th and 86^th streets because there is no place to park now anyway,” said Marc V. Shaw, the commission chairman (and former first deputy mayor). “Mainly, it gets rid of the issue of creating a parking nightmare north of 86^th Street, especially in Harlem, and it more better defines the traditional downtown and midtown business districts.“

Shrinking the zone would not make as big a dent in “vehicle miles traveled” (a 6.2 percent reduction compared to a 6.7 percent decline under the Mayor’s plan) and would also reduce the amount of revenue (from $420 million to $387 million), according to city Department of Transportation estimates. The adjustment, which won’t be voted on unless presented as part of the final recommendation in January, shows that the clout of uptown legislators trump the Mayor's ideas about his own neighborhood.

To whet your appetite, we asked the host, Scott Turner (himself an Atlantic Yards opponent and blogger), for some sample questions:

Word is, Norman Oder could play with one arm tied behind his back--and still win!

“The subject of the conversation moved to my swap idea, and they were interested in discussing it, which was the whole point of them calling the meeting,” Mr. Sprayregen, whose family owns four Tuck-It-Away storage warehouses in the expansion footprint, told The Observer. “I told them I would be prepared to provide more details if indeed it is something in conceptual form that they would be prepared to entertain. That’s the way it was left, basically with us agreeing to get together again. In the meantime, they will continue doing their thinking and they asked me to give them more details of the swap.”

The university's overture would help remove any possible objection that City Council members might have against the expansion with just a few weeks to go before they vote on the project. If successful, the swap might also help meet one of the university's recently announced goals: new housing for university affiliates to alleviate the influx of new residents that the expansion is expected to create.

In September, Mr. Sprayregen outlined “the swap” for The Observer: He trades three properties west of Broadway for two properties Columbia owns to the east. Mr. Sprayregen would end up with more total land mass but would save the university the trouble of going through eminent domain.

He said the university, represented at the meeting by Robert Kasdin, senior executive vice president, and Bill Lynch, a lobbyist, wanted more details about how many apartments Mr. Sprayregen would want to build on the new site and how many would be affordable. He said he expected they would meet again before the holidays.

The park idea came about during negotiations with Borough President Scott Stringer, who listed it as part of the “historic agreement” he reached with the university in September. But the New York Post’s coverage of the issue really made it seem pretty unseemly: an Ivy League university pushing out a historically black institution from Harlem, of all places.

“There was a general sense that we heard that it would be a good idea to turn it into a park and then people took a closer and decided that was not the way to go,” Robert Kasdin, senior executive vice president for Columbia, said today outside a City Council public hearing on the university’s expansion. “We never planned to have academic buildings there.”

Originally, the idea was to build retail on the triangle of land at 125^th Street and 12^th Avenue, which would have allowed the Cotton Club to retain its current location in a new building.

It would be the first time in more than three years. At that time, Mr. Sprayregen made it clear he did not want to sell his properties to make way for the university’s expansion as long as Columbia was threatening eminent domain.

“I want to keep my properties where they are,” Mr. Sprayregen told The Observer today outside of a City Council public hearing on the expansion. “Failing that, I would entertain a swap of a few properties across the street so that I can remain in the community. But besides that, unless they want to first take eminent domain off the table or are forced to, I do not want to negotiate my removal.”

He said he did not know what Columbia wanted to discuss, but that he received a call a few days ago from the office of Robert Kasdin, the university’s senior executive vice president who is in charge of the expansion. He outlined the property trade he is thinking of to The Observer and other newspapers back in September, but has not approached the university with the idea directly.

Columbia does not, as a rule, comment on negotiations. However, earlier today, Mr. Kasdin said to the City Council that the school had decided not to acquire the Cotton Club and turn the property, at 125^th Street and 12^th Avenue, into a park as it had considered doing earlier this fall, but instead would preserve the famous music venue at the current location somehow.

Once there was the West Side Stadium. Now there are the West Side rail yards.

Once there was Atlantic Yards. Now there is Moynihan Station.

For just about each of Deputy Mayor Dan Doctoroff’s early development projects, there is now another similar one wending its way through a review process. The new one may be just as ambitious--and controversial--as the old, but it is infused with a vastly different sensibility, more patient in its approach, more responsive to the grass-roots community.

As he is about to step down as deputy mayor for economic development and rebuilding, Mr. Doctoroff eschews the idea that he or the Bloomberg administration went through a sea change in the way they approached development over the past six years. But it is hard to deny that he is, if not exactly more conciliatory, at least smarter about what he wants and how to get it.

“It is fair to say that we have become better listeners, and we have reached out earlier and more often to the State Legislature,” Mr. Doctoroff told The Observer in a telephone interview on Dec. 10. “On the other hand, we would not say that we did not go out and promote our ideas before. We have gotten better at it. I would not say there has been a dramatic shift.”

Still, what a shift there has been. On June 15, 2005, the Bloomberg administration announced that it supported a new Yankee Stadium. Without further ado—and in a process critics say ramrodded the project through—eight days later, it got the Legislature to set aside the park land where the ball team would build it.

By contrast, the mayor announced on Nov. 8 of this year that the city wanted to swap park land to make way for a new amusement district in Coney Island. It will hold a couple of public meetings about it, and then leisurely ask that park alienation be introduced in Albany in January, and the city expects that it will take until June to get it passed.

Here’s another example: The same rail yards where city and state taxpayers were supposed to build a platform and allow the New York Jets to build a new stadium is now the subject of a complex private-public, City Hall-Metropolitan Transportation Authority arrangement. This time around, a combination of offices, apartments and stores will be built (along with a new school, a couple of parks and a cultural facility) by a private developer, chosen through a competitive process, who will give a few hundred million dollars to the transit agency’s capital budget; build the platform on his own dime; preserve most if not all of the High Line, the old elevated train track turned park; and put aside a few hundred apartments for low-income families.

Mr. Doctoroff suggested that each of these projects has to be treated independently, and that the process—i.e., the level of community involvement—would vary.

“You cannot take a cookie-cutter approach,” he told The Observer. “Sometimes you have to seize the opportunity and still provide the community input that it deserves.”

But he also added that one of the lessons he learned is that ULURP—the name for the city rezoning process—works. The deliberative, and at times contentious, seven-month review procedure takes a project through a community board, a borough president, the City Planning Commission and, finally, the City Council—with a public hearing and vote at each step.

THIS IS QUITE a change from a few years ago, when Mr. Doctoroff and then Governor George Pataki decided to take the West Side Stadium through a state process that avoided the possible contention of city politics. But it was in Albany where Assembly Speaker Sheldon Silver killed it; a majority of City Council members ended up supporting the idea.

There is one other project like that—although it ended up getting Mr. Silver’s approval—that Mr. Doctoroff now has second thoughts about.

“I look back on Atlantic Yards,” he said. “I am a huge believer in the ULURP process. I think it makes sense. It allows the issues to be aired in an appropriate way. If it happened again, and the state were to ask if I would encourage them to take Atlantic Yards through the ULURP process, I would say yes.”

Mr. Doctoroff pointed out that, by contrast, the plan now is to take Moynihan Station, a new transit complex in western midtown, through ULURP, even though the state has bought property and plans to lease it to a private developer. When Atlantic Yards—a basketball arena and apartment village in Brooklyn—avoided ULURP, the argument was that since the train yards on which it would be built were owned by the state, it should be handled exclusively by the state.

As it happened, Mr. Doctoroff oversaw the rezoning of 78 other neighborhoods that did go through ULURP—meaning that they received the consent of the City Council. Mayor Bloomberg, in announcing his right-hand man’s departure from government (and his re-entrance into the private sector as president of the mayor’s media company, Bloomberg L.P.), said Mr. Doctoroff was more effective than any economic development official since Robert Moses while being far more sensitive to community concerns.

Alex Garvin, an architect who worked as the managing director for planning for the Olympics bid in 2005, said that Mr. Doctoroff became savvier about the way government operated.

“I think his experience with government and what existing agencies can and cannot do has changed over time,” he said. “A lot of the things which we proposed were long shots from the beginning, and nobody would have been surprised if they either happened or didn’t happen. Dan tends to pick out things that are worth fighting for.”

The stadium defeat, as humbling as it might seem to an outsider, actually set up Mr. Doctoroff’s next big project: PlaNYC, a collection of 127 initiatives to make the city more environmentally friendly, chief among them, congestion pricing. It may have been a coincidence that the city that actually won the 2012 Olympics had pioneered this system of charging cars for entering the city’s business district, but it wasn’t exactly coincidental that London had an equal, or greater, reputation for livability as New York.

“When I was traveling around the world understanding how they were evaluating the different cities that were bidding, I also gained a much deeper understanding about what New York’s competitive strengths are,” Mr. Doctoroff said. “It reinforced this view that New York is in a fierce competitive battle for employers, residents and visitors, and we have to continue to strive to think about the city’s future and prepare for it with the way we use land, the way in which we use infrastructure, the way in which we serve residents and businesses, the way in which we treat our environment. I am constantly aware of the way in which other cities emulate New York, and if we don’t stay out ahead, there will not be a very happy result.”

Mr. Doctoroff, in fact, ended up commissioning a $523,000 report shortly after the failed Olympics bid on how the city could stand its ground against London; according to the report, 32 percent of senior executives surveyed found that London was a better place to live than New York, while 30 percent thought the opposite.

Congestion pricing was supposed to help by raising money to build out the transit system and discourage commuters from using cars. It, and the whole PlaNYC, came about through a deliberate, open process in which Mr. Doctoroff’s staff held dozens of meetings with officials, community groups and regular citizens. The mayor set up a panel of labor leaders, real estate representatives, planners, environmentalists and City Council members to mull the issues over. And yet, despite all that foundation work, once the mayor announced his support for congestion pricing in April, it ran into the same problem that the stadium did: resistance from Mr. Silver and colleagues in the State Assembly. Could it be that Mr. Doctoroff made the same mistake twice?

Mr. Silver, Governor Spitzer and Mayor Bloomberg eventually worked out a compromise, sending the congestion pricing issue to a commission made up of representatives from all levels of government that will recommend a congestion mitigation plan by the end of January. It is, for matters that are not about land use, the next best thing to ULURP. Mr. Doctoroff, this time, will be watching from the sidelines to see if it works.