For nearly a century, the Supreme Court has made it difficult for a president to defy the clear text of a law passed by Congress. The court prevented Franklin D. Roosevelt from firing a leader of the Federal Trade Commission in 1935. It stopped the Reagan administration from defying a pollution investigation in 1988. It helped block Barack Obama’s attempt to expand immigration protections in 2016.

The decision Monday allowing President Trump to fire F.T.C. commissioners represents a break with this history. The ruling dismisses longstanding precedent and effectively discards a 112-year-old law that said the president could fire commissioners only for “inefficiency, neglect of duty or malfeasance in office.” Mr. Trump can now fire commissioners in regulatory agencies simply because he wants to.

The majority opinion by Chief Justice John Roberts says that requiring presidents to have cause when they fire agency heads conflicts with the separation of powers in the Constitution. Because the F.T.C. exercises executive power, it “must therefore be controlled by the chief executive,” Mr. Roberts wrote. The majority has decided that Congress erred when it tried to insulate the F.T.C. and a couple of dozen other agencies from partisan politics by stipulating that its leaders be semi-independent. The ruling happens to suit perfectly the view of President Trump, who has said that Article II of the Constitution gives him “the right to do whatever I want as president.”

Perhaps the clearest sign of the ruling’s weakness is that the six justices in the majority — the six appointed by Republican presidents — do not even have the courage of their misguided convictions. In another ruling Monday, the court rejected President Trump’s bid to fire Lisa Cook from the Federal Reserve Board. In this case, Mr. Roberts denied Mr. Trump’s bid to fire Ms. Cook with only a thin pretext of cause and no notice or hearing. Allowing the firing, Mr. Roberts wrote, would require an “interpretive leap out of step with the statute Congress enacted and our nation’s tradition of central banking protected from political interference.” The vote was 5 to 4, with the chief justice joined by the court’s three liberals and Justice Brett Kavanaugh. The ruling sent the case back to the lower courts. Ms. Cook must receive due process to dispute the charges against her, and then a lower court will evaluate Mr. Trump’s claimed cause, the court ruled.

It is a good outcome. Though the case will continue, the court is effectively disposing of Trump’s bid to end the Fed’s independence. But why is the statute Congress enacted to protect the Fed from political interference worth upholding but not the law that established the F.T.C.? Justice Amy Coney Barrett, dissenting in the Cook case, pointed out that the two holdings are in “serious tension” with each other. “How can history support both a categorical rule and a carve-out?” she asked. There is no answer.

In truth, the main distinction is that many Republicans care more about a well-functioning Fed than about any other agency. Other agencies often regulate businesses and individuals in ways that free-market conservatives oppose. The Fed has regulatory powers too — which makes the carve-out all the more questionable — but also sets monetary policy and thus affects the health of financial markets. Today’s decision effectively limits the president’s ability to roil those markets while giving him wide latitude to fire regulators who monitor corporate excess.

The logical flaws in the opinions continue a worrisome pattern with the current Supreme Court. The six Republican-appointed justices do occasionally stand up to Mr. Trump’s abuses of power, including his attempt to enact unilateral tariffs (another policy, notably, that corporate America did not favor). But they are inconsistent in their defense of the Constitution. They give Mr. Trump wider latitude than they gave President Joe Biden or Mr. Obama.

Most worrisome, the Supreme Court is bestowing new powers on a president who often behaves as an aspiring autocrat, defying bipartisan tradition and even the law in the pursuit of personal authority.

Today’s decision springs from a conservative idea known as the unitary theory of the executive. The theory holds that nearly all power in the executive branch ultimately comes from the president. Voters have chosen only the president, along with the vice president, to run the executive branch. And the Constitution delineates three separate branches of government, which means that Congress should not be able to pass laws restricting the president’s ability to fire or hire officials working in regulatory agencies such as the F.T.C., according to this view.

Proponents of the unitary theory believe that the executive branch has mushroomed into a vast, unaccountable bureaucracy in which even a president can struggle to implement policies. This concern is partly reasonable. Presidents of both parties have shared it in their own ways. Creating a nimbler and more responsive executive branch would be a worthy project.

Yet the unitary theory ends up being more radical, and more disruptive to the previous understanding of the separation of powers, than its advocates typically acknowledge. There is no question that Congress has some authority over regulatory agencies. The Constitution gives the Senate confirmation power for top positions, for example. Mr. Roberts says this merely gives the Senate the power to confirm or reject the appointees that the president prefers. But this view throws out nearly a century of practice that Congress put in place because it saw bipartisan composition as a strength for agencies.

The 1914 law creating the F.T.C., for example, stipulates that no more than three of the agency’s five commissioners can come from one political party and that the president can fire a commissioner only for certain reasons. When the Supreme Court unanimously blocked Roosevelt from firing a conservative F.T.C. commissioner in 1935, it cited this language. That precedent has governed every president since.

The current court, by contrast, looked at the same law and decided it was an unacceptable infringement on presidential authority. The decision is especially jarring coming from conservative justices who insist that they defer to the text of statutes and to the constitutional power of Congress. In this case, the justices ruled that both were irrelevant.

“Seldom, if ever, has this court worked such a profound bait-and-switch on a coequal branch,” Justice Sonia Sotomayor wrote in her dissent. “For more than 90 years, Congress believed, with this court’s express approval, that it was allowed to create a workable government, including by granting certain agencies tasked with certain responsibilities some independence from presidential control.”

With the new ruling, the court is creating a super-empowered presidency — outside of the Fed, that is. A president will now be able to fire officials at a range of agencies that had previously had some protection from politics. Many of these officials have expertise in their fields. The list of such agencies includes the National Labor Relations Board, the Securities and Exchange Commission and the Federal Communications Commission.

Central to the success of the American experiment over nearly 250 years has been the balance of powers among the three branches of government. Together, Mr. Trump and this Supreme Court are upsetting that balance. They are deviating from a tradition that has lasted more than a century, in which parts of the government operate with bipartisan leadership removed from everyday partisan politics, as Congress intended. The effect is to sideline Congress, which the authors of the Constitution viewed as the primary branch among equals. The Supreme Court today created a government run by a very small number of people who work at either the Supreme Court or the White House.