The World Trade Center saga has turned from tragedy to triumph to soap opera.

Thirteen years after 9/11, the story has taken a melodramatic turn.

Downtown Manhattan has a slightly higher vacancy rate than Midtown — just under 13% versus 11%. But the larger availability is due mainly to the sudden addition to the market of new 4 World Trade Center’s 2.3m sq ft and Merrill Lynch’s exit from Brookfield Place.

Otherwise, Lower Manhattan is hot. In addition to Condé Nast at 1 World Trade Center, media tenants are moving from uptown, lured in part by rents of $50-$60/ sq ft compared with $70-$80/sq ft further north.

Time Inc recently signed for 550,000 sq ft at Brookfield Place, abandoning its historic home on Sixth Avenue in the Rockefeller Center. Also, the gargantuan, Santiago Calatrava-designed train station at the World Trade Center site is nearing completion after a decade of delays and cost overruns.

Yet two awkward dramas have unfolded. Larry Silverstein, who seemed poised to build the 80-storey 3 World Trade Center, said he needed a loan guarantee from the Port Authority (PA) of New York and New Jersey, which owns the land. A signed, 516,000 sq ft lease with GroupM wasn’t enough to secure a construction loan for the 2.5m sq ft tower.

Silverstein and the PA have bumped heads often in the past. What made this time different is a scandal that’s paralysed the PA. Unannounced entrance lane closings to the PA-controlled George Washington Bridge last December, nominally for a “traffic study,” were found to be an act of retribution by New Jersey Governor Chris Christie’s aides aimed at the mayor of Fort Lee at the bridge’s foot.

The closure caused three days of havoc. The ensuing uproar crippled Christie’s presidential aspirations and sent the PA into a tailspin. Several top commissioners were forced to quit and the agency is under investigation by the authorities. The crisis left the normally secretive but disciplined PA board rudderless which, combined with specious claims of an office “glut” downtown, has paralysed deliberations to the point that the PA has postponed voting on Silverstein’s request three times.

The stalemate revived old complaints. Is Silverstein greedy? Does downtown need so much new office space? The dispute comes at a watershed moment as Manhattan’s office-leasing momentum shifts away from Midtown. High-profile relocations are creating a new, high-rise neighbourhood at Hudson Yards.

Downtown’s commercial scene seemed on the verge of a definitive recovery from 9/11 until the 3 World Trade Center funding issue came up. It threatens to scuttle the GroupM deal and to leave “ground zero” with only two of the four planned office skyscrapers built.

Silverstein’s cause appeared to suffer a further blow two weeks ago when Douglas Durst, the PA’s partner in 1 World Trade Center, said soft demand had forced him to reduce asking rents from the $80s to the $60s. The “iconic” skyscraper was just over 50% leased and had not signed a new tenant in more than two years.

Silverstein’s critics pounced on Durst’s downbeat remarks to argue that so weak a market made 3 World Trade Center unnecessary. But that day a tech firm called Kids Creative signed a lease for the entire 88th floor of 1 World Trade Center at more than $90 per sq ft - the highest rent ever paid downtown. Meanwhile, another tech firm, Percolate, is believed to be close to a deal for 50,000 sq ft.

As the battle rages over 3 World Trade Center, Silverstein is on the brink of a breakthrough at 4 World Trade Center: a near-certain lease for 120,000 sq ft with software developer MediaMath. It would be the tower’s first private-sector lease; 1.2m sq ft were pre-committed by government agencies, including the PA itself.

In May the office tower drama was upstaged by the opening of the 9/11 Memorial Museum after years of delays and was proclaimed a heart-wrenching, cathartic masterpiece. It was a welcome step toward making the 16-acre site seem more realised.

The mood changed, though, when it was revealed the museum — home to horrific 9/11 artifacts and even to human remains — included a gift shop selling tacky souvenirs, including a USA-shaped cheese plate with little hearts marking where the terrorist planes struck.

Then came word that famed New York restaurateur Danny Meyer would launch a café inside the museum; that it would offer “New York-made draft beers and American wines on tap” offended many. I wrote that a “bar and grill” was inappropriate at the site where nearly 3,000 were killed, in a museum filled with ruined fire trucks and photos of office workers falling to their deaths.

As of now plans for the café are still on.

All the controversies recalled the difficult years soon after 9/11 when no one could agree on what the new World Trade Center should be. But vigorous public contention is built into New York City’s DNA. The noisy, untidy deliberations gave way to progress — and better results than seemed possible 10 years ago. Today’s renewed belligerence might well portend just as welcome an outcome.

Steve Cuozzo is a real estate columnist and contributor at the New York Post