By reaching an agreement with California, the auto companies want to avoid a situation in which the Trump administration requires one thing, and California (with the dozen or so states that usually follow it) requires another. The fear is that a divided market would, at a minimum, put automakers to the trouble and expense of certifying they meet two different sets of standards, and, at worst, manufacturing different vehicle models for different markets. Other auto companies also reportedly expressed interest in the California alternative. The settlement sidestepped the president’s plan, reportedly enraging him.

Antitrust prohibits companies from conspiring to restrict competition. But under well-established legal principles, they may jointly lobby government for rules they prefer, and comply with those rules once adopted. And companies may independently and unilaterally meet whatever voluntary standards they wish.

The Justice Department’s antitrust division has a long and proud history of independence from the White House. But circumstances surrounding the investigation have raised suspicion that its motivation is less than pure. It may succeed in squelching the California initiative through intimidation. For emphasis, lawyers for the Transportation Department and the E.P.A. sent a menacing letter to California officials warning that the state’s agreement with the car companies appears to violate federal law.

All this adds uncertainty and delay over the rules the auto industry must follow. Now, the question of whether the E.P.A. can revoke a waiver it has already granted will be thrown to the courts, along with the administration’s theory that, regardless, California’s greenhouse gas standards illegally conflict with the Transportation Department’s authority, questions that may take perhaps years to resolve. And if the Justice Department’s investigation progresses, it could produce a blockbuster antitrust lawsuit. All of these conflicts could wind up in the Supreme Court.

This mess is the opposite of what the auto companies want. They supported the Obama standards and joined the administration in federal court to defend them because they delivered certainty and predictability. Since they took effect, automakers have steadily produced cleaner models while enjoying some of the best sales years in history.

At the same time, the transportation sector is responsible for the largest and fastest-growing share of greenhouse gas emissions in our economy. Ambitious national standards are even more critical for this industry than in the electricity sector, where cheap natural gas and a surge in renewables are helping to reduce emissions.

The auto industry is not looking for the drastic rollback that Mr. Trump seems determined to deliver. The White House has repeatedly pressured auto company chief executives to support his plan, yet not one has publicly endorsed it, and several have defected. The industry’s trade association has said it remains committed to increasing fuel economy and strongly supports a program aligning federal and California standards. To stay competitive globally, companies know they must develop the next generation of fuel-saving technologies here in the United States.