What’s a federal agency to do? Twice in the last eight years, the Environmental Protection Agency has issued carefully vetted rules aimed at reducing air pollution that crosses state lines — the smog-forming nitrogen oxide pollutants and health-threatening sulfur dioxide that drift eastward from Midwestern power plants. And, in both cases, the agency has been shot down by the United States Court of Appeals for the District of Columbia.

The first rule, issued in 2005, was aimed at reducing these pollutants by up to 70 percent. Unlike most programs of the George W. Bush administration, it won swift approval from environmentalists. But it was struck down by a three-judge panel in 2008 for largely technical reasons, one of which was that the complex emissions trading system it established could allow some states to escape their obligations to cut emissions.

In July last year, the agency finalized a rule that addressed the glitches while requiring even greater pollution reductions. Several power companies and states sued, and, this week, another three-judge panel discovered flaws — including, again, in the trading system. It also said the rule had violated the Clean Air Act by imposing federal standards on polluters before the states could develop their own plans.

In an unusually blistering dissent, Judge Judith Rogers, who had joined in the 2008 ruling, said that the agency had acted well within its jurisdiction under the Clean Air Act, had done just what the court had asked of it and had been “blindsided by new arguments raised for the first time by this court.” The E.P.A. now confronts a choice. It can return to the drawing board, or better yet, appeal the ruling. Another plan could take three or four years to develop. And, in that time, Americans will continue to pay the price of pollution.