The new Barclays Center arena in Brooklyn opened in late September, garnering cheers from elected officials, most architecture critics and guests who have gone to see Jay-Z, the Rolling Stones and the revamped Brooklyn Nets, relocated from New Jersey and contenders in their NBA division.

However, the story behind the arena, and the larger $4.9 billion Atlantic Yards project, slated to include 16 towers over 22 acres, is darker. In New York, the government has supplied far less direct subsidy than in other jurisdictions — just look to Miami, which paid for more than 80 percent of the Marlins’ new stadium—but the overall deal still shows how the public interest can be clouded when government agencies welcome a new “hometown team” and an ambitious development tethered to a sports facility.

The nine-year battle to build Atlantic Yards is steeped in controversy: over public support via subsidies, tax breaks and low-cost land; over the use of eminent domain to remove recalcitrant residents; over a bypass of local elected officials (given that the project was supervised by an unelected state agency) for Brooklyn’s most expensive real estate project; and over a persistent lack of accountability.

The project, its defenders point out, has survived several legal challenges. (Well, except for a court ruling, upheld this year, that cited a “failure of transparency” and forced the state of New York to do something it chose not to do three years ago: study the environmental impact of a potential 25-year project buildout.) Still, the legal bar regarding issues like eminent domain and environmental review in New York is low.

What we have seen is cozily cooperative behavior by powerful Brooklyn-based developer Forest City Ratner and government agencies. It seems fitting that Forest City’s partner on the arena is Nets majority owner Mikhail Prokhorov, whose ascension to wealth included self-admittedly corrupt activities (neither unusual nor illegal in post-Soviet Russia).