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Galloo Island, in Lake Ontario, seemed to be a prime spot for a wind farm. It is mostly deserted and sits about six miles offshore in northern New York, so few people were likely to be bothered by the looming turbines and their relentless whoosh.

Then a hunter spotted an eagle’s nest.

The discovery kicked off a fight over the safety of birds and accusations of a cover-up that have stalled the project. A judge has questioned the integrity of one of the country’s largest wind farm developers, and a pair of eagles seems to have disappeared.

The case demonstrates the challenges facing Gov. Andrew M. Cuomo’s clean energy goals, which last week were enshrined in an ambitious new law requiring 70 percent of the state’s electricity to come from renewable sources, such as wind, solar and hydropower, by 2030. The state has particularly high hopes for wind power.

But currently, only a bit more than 3 percent of the state’s electricity comes from large-scale wind projects. That number has hardly budged over the last five years despite billions of dollars in available subsidies and plenty of willing developers.

Developers and other energy groups blame the state’s cumbersome approval process — the result of a 2011 law — and reluctance to overrule local opposition and zoning ordinances.

“There needs to be a greater sense of urgency to get these projects built,” said Anne Reynolds, the executive director of the Alliance for Clean Energy New York, whose membership includes clean energy developers and environmental groups.

But Galloo Island shows that expanding renewable energy — with massive infrastructure that affects communities and wildlife — involves more than overcoming bureaucratic hurdles.

The project was supposed to be a relatively easy one to get approved. The island’s main inhabitants are a retired couple who act as caretakers for the wealthy family that owns most of it. There was little local opposition when Apex Clean Energy, one of the country’s largest wind power companies, started planning in late 2015 to put up at least two dozen turbines, each almost 600 feet tall.

Then a bald eagle’s nest appeared, sitting high in a linden tree.

In spring 2017, Apex learned about the nest from the island’s caretaker, according to documents Apex filed later with the state.

The presence of eagles would not necessarily have doomed the project. The population, while still protected, has rebounded nationally, and the U.S. Fish and Wildlife Service has encouraged wind developers to avoid prosecution for killing eagles by applying for licenses to cover the number of birds who might be struck by wind turbines.

But the nest, which eagles use almost exclusively for raising their young, promised new hurdles. At a minimum, the discovery could lead to additional studies and plans for monitoring the nest and the flight paths of any eaglets. Environmental regulators tend to be more protective of nesting bald eagles because they reproduce slowly.

A consulting firm for Apex dispatched a biologist to the island in April 2017. The biologist found the nest with an adult eagle atop it, according to a document reviewed by The New York Times. Later that month, Apex commissioned a helicopter to inspect the nest, which appeared empty, Apex later said.

But when Apex submitted its application to the state in late 2017 to build the wind farm, it said there were no known bald eagle nests on the island, according to public documents reviewed by The Times.

With their soaring majesty and fierce visages, bald eagles are not easily kept secret, even on a remote island. In 2017, a hunter had spotted the nest. He took photos, which eventually reached Clif Schneider, a retired biologist.

Mr. Schneider, 76, had spent much of his professional life studying and safeguarding the area’s fish population for the state Department of Environmental Conservation. He had been worrying about global warming for decades and believed drastic action across the globe was needed. He did not believe a few wind turbines would solve the problem.

Like many upstate residents, he was troubled that New York City gobbled up fossil fuels but did not have to deal with the blight of giant machinery on the landscape.

Mostly, though, he was worried about the turbines killing birds. Just off Galloo Island is Little Galloo, a small, denuded island that is home to tens of thousands of nesting birds.

Mr. Schneider did not expect to stop the project, but he thought he could push for some constraints on the turbines, such as limits during migrations. Because state law requires energy developers to provide money to affected local communities, Mr. Schneider was able to hire avian experts to help challenge the project. He accused the company of lying about the eagle’s nest.

“It is really disconcerting,” Mr. Schneider said. “It just destroys trust. They should have reported it immediately. They should have been truthful in their application.”

Steve Bowers, a spokesman for Apex, acknowledged the company should have been open about the existence of the nest, but said it did not have enough evidence at the time to establish the nest was being used.

“We should have simply disclosed all relevant information,” Mr. Bowers said.

One judge reviewing Apex’s application said the episode raised “serious questions about the applicant’s character and fitness.” State energy regulators said in December 2018 that “significant consequences appear to be warranted.”

Apex withdrew its application for the project in February, saying it may consider restarting it in the future. Apex says it has spent more than $20 million trying to develop three wind projects in New York, including Galloo, and that two of them are stalled.

There are about two dozen large-scale wind farms in New York. More wind capacity was built between 2005 and 2010 than in the years since, and no new wind farms are under construction, Ms. Reynolds, of the Alliance for Clean Energy, said. Some are in the pipeline, and the state is weighing proposals for major wind farms miles off the Long Island shore.

Doreen Harris, a senior official at the New York State Energy Research and Development Authority, which provides state subsidies to renewable energy projects, said she believed the application process was improving. There is wind farm construction scheduled for next year, she added.

“I feel really confident and optimistic about reaching our goals,” Ms. Harris said.

Concern over the eagles has continued. A couple of months ago, in April, Mr. Schneider and his partner checked on the nest. Through binoculars, they spotted two eagles there, they said. They grew excited about the possibilities of eaglets.

Apex, hoping to revive the project, had also been monitoring the nest and the local eagle population. The company planned several helicopter flyovers; state officials told Apex not to get within 500 feet of the nest.

Low-altitude flights can spook animals. In North Dakota, a family said that one Apex flight looking for eagles’ nests there in March stirred panic among livestock that killed two calves, according to Tri-State Livestock News.

Not long after Apex conducted one of its latest flights over Galloo Island, Mr. Schneider returned with his boat for a visit. The eagles were not there, he said. Several more visits have failed to turn up any sign.

Gerald Smith, an ornithologist who aided Mr. Schneider’s efforts to challenge the project, believes the helicopter scared the eagles away for good. “They destroyed an active eagle’s nest,” Mr. Smith said.

Mr. Smith said he wondered if Apex intended to drive off the eagles, clearing the way for another attempt to build.

Mr. Bowers, the Apex spokesman, said that was not the case. The flyover was conducted “to further clarify the potential environmental impact of the project,” he said.

For the moment, there are neither wind turbines nor bald eagles on Galloo Island.

Sheelagh McNeill contributed research.

Joseph Goldstein writes about policing and the criminal justice system. He has been a reporter at The Times since 2011, and is based in New York. He also worked for a year in the Kabul bureau, reporting on Afghanistan. @JoeKGoldstein

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