“America has reached a fork in the road, and the time has come to make a decisive choice,” Daniel J. Popeo, chairman of the Washington Legal Foundation, wrote this week in his monthly column in The Washington Examiner. The choice he posited was between continuing to endure judicial intervention in the conduct of the war on terrorism and “returning control over national and homeland security decisions to the executive and legislative branches.”

I don’t mean to single out the Washington Legal Foundation, a respected conservative research and litigation organization. It is hardly alone in its ritualized framing of a dichotomy between law and national security.

And that’s the point. That the courts — and the lawyers who bring cases to them — are a threat to the country is a trope that has penetrated deep into public consciousness. The typical accompanying warning against “Miranda rights for terrorists” resonates with the doom-saying of an earlier generation of conservatives to the effect that courts make it impossible to keep the streets safe from common criminals.

Now, as then, politicians who would stand up for the courts do so at their peril, or presumed peril. Mark the Obama administration’s painful indecision about what to do with the self-described mastermind of 9/11, Khalid Shaikh Mohammed, as Exhibit A. A New York jury’s acquittal this week of Ahmed Ghailani, the accused embassy bomber, on all but one of many charges provided an utterly predictable platform for Republican politicians to denounce the use of civilian courts to try terrorism cases.

I’m not running for anything, so perhaps it’s easy for me to stand up for the courts. But I like to think I would do it anyway, because the current court-bashing is so deeply misguided. It reflects a profound failure of imagination: the inability to imagine how the world would look — or, more precisely, how the United States would look to the world — if the Supreme Court back in the dark winter of 2003-2004 had refused a hearing to the detainees at Guantánamo Bay.

The Bush administration tried to argue that no legal process was due the detainees, and in fact that the federal courts lacked jurisdiction even to hear any case arising from the Guantánamo detentions. But the justices nonetheless accepted the case, Rasul v. Bush; heard it days before the news broke about the atrocities at the Abu Ghraib prison in Iraq; and ruled in June 2004 that the federal courts did indeed have jurisdiction through habeas corpus to hear the detainees’ claims that they were being wrongly confined without formal charges or the prospect of a hearing. (Given the politically polarized nature of today’s debate, it is perhaps worth pointing out that four members of the 6-to-3 majority had been appointed by Republican presidents.)

Nine days later, the Bush administration responded to the decision by putting in place a system of “combatant status review tribunals” to determine whether each detainee had been designated correctly as an enemy combatant. These tribunals, staffed by three military officers, were deeply flawed; detainees were not represented by lawyers and had sharply limited rights to see the government’s evidence. But the new system was an acknowledgment, however grudging, that there was such a thing as the rule of law. It would not have happened without the Supreme Court.

This is not the place to recount the convoluted, problematic, and still unfinished evolution of the Guantánamo detention policy. But looking back to the 2004 decision and those that followed, including the 2008 Boumediene decision in which the Supreme Court rejected a Congressional effort to strip the courts of jurisdiction, it seems abundantly clear that the court did the country a huge favor. In making the rule of law part of the conversation, it saved the other two branches from their own worst instincts and, in doing so, redeemed at least a bit of the national honor that had been so recklessly squandered.

Although it has now been more than two years since the Supreme Court addressed a Guantánamo-related issue, the law has continued to develop in the hands of federal judges in Washington. Judges of the Federal District Court have issued more than 50 habeas corpus decisions, with the detainee prevailing in about three-quarters of the cases. People can debate whether all these decisions were correct by any given measure; the United States Court of Appeals for the District of Columbia Circuit has upheld some, overturned others, and most recently, vacated one and sent it back for further consideration. The appellate decisions themselves have not been without controversy.

But my point is that here, again, we owe the judges a debt of gratitude. Acting without guidance from Congress and with hardly any from the Supreme Court, judges across all ideological lines have approached a thankless task with utmost seriousness and attention to the details that matter, striving to extract a legal regime from an episode born in lawlessness.

Once again, the courts saved the other branches from their own worst instincts. In a dozen habeas cases that the government contested and lost, the Obama administration chose not to appeal. One was the case of Mohammed Jawad, a teenage detainee (perhaps as young as 12 when he was captured in Afghanistan in 2002) held for nearly seven years until Judge Ellen S. Huvelle of Federal District Court ordered his release in July 2009. Judge Huvelle found that the government had produced no evidence to justify continued confinement; she had earlier thrown out a purported confession as the product of torture. At a hearing that preceded her final decision, Judge Huvelle called the case “unbelievable,” “riddled with holes,” and “an outrage.” The next month, the administration, which until then had defended Mohammed Jawad’s detention, repatriated him to Afghanistan.

For anyone for whom it is not a full-time job, it is almost impossible to keep track of the Guantánamo cases as they work their way through the courts. The news media have not been much help; The Times, for example, did not report on a significant appeals court decision earlier this month in the case of Mohammedou Ould Salahi (a Guantánamo detainee from Mauritania, not the White House party-crasher with the same last name from northern Virginia.) The public inattention is unfortunate, because it is in decisions like Salahi v. Obama that the judicial process reveals itself.

The decision vacated the district court’s grant of habeas corpus and sent the case back for reconsideration of whether Mr. Salahi, who had sworn an oath of allegiance to Al Qaeda in 1991, was still “part of” the organization, despite his assertion that he had long since “severed all ties” by the times he was captured in Mauritania 10 years later.

Early this past summer, weeks after Judge James Robertson had issued his habeas corpus ruling in the Salahi case, the law within the District of Columbia Circuit continued to evolve. In a trio of decisions in other cases, the appeals court refined and, to some extent, redefined what it means to be “part of” Al Qaeda and thus subject to detention under the Congressional Authorization for the Use of Military Force. As a result, a different federal district judge (Judge Robertson having retired) will now have to apply the revised definition to re-evaluate Mr. Salahi’s claim that he is being illegitimately held.

The definitional details, while significant for the law, are not necessary for this column. The three-judge appellate panel’s decision in the Salahi case was unanimous, and that is an important point. The decision was written by Judge David S. Tatel, one of the court’s more liberal members, and joined by Chief Judge David B. Sentelle and Judge Janice Rogers Brown, two of its most conservative.

I very much doubt that anyone, even a politician, who actually took the trouble to read this nuanced opinion could go out on the stump to denounce the federal judiciary for unduly interfering with the prerogatives of the other branches or the prosecution of the global war on terrorism. In this season of Thanksgiving, let’s thank the courts.