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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.