Before 9/11, judges had no power to entertain writs of habeas corpus (petitions for release) by enemy fighters taken into custody by U.S. forces overseas.

Justice Robert Jackson spelled out this rule in a landmark 1950 decision, Johnson v. Eisentrager: "We are cited to no instance where a court, in this or any other country where the writ [of habeas corpus] is known, has issued it on behalf of an alien enemy who at no relevant time and in no stage of his captivity has been within its territorial jurisdiction. Nothing in the text of the Constitution extends such a right, nor does anything in our statutes."

That might still be the law had the Bush administration given the hundreds of suspected "enemy combatants" whom it sent to its Guantanamo Bay prison camp in and after 2002 a fair opportunity to show that they were innocents seized and held by mistake, as many apparently were, an almost inevitable feature of this war against terrorists who masquerade as civilians.

But instead, the Bush team seized on its presumed freedom from judicial oversight, spurned the advice of military lawyers, and denied the detainees any semblance of due process, while subjecting some of them to brutal interrogations.

These bad policies have led to muddled law. Understandably offended by President Bush’s approach and the black eye that it was giving America overseas, the Supreme Court deep-sixed Johnson v. Eisentrager and ruled for detainees in three cases culminating in a 5-4 decision last June asserting broad judicial power to hear petitions for release from Guantanamo.

In the process, the justices struck down parts of two recent acts of Congress and assumed unprecedented, open-ended, and potentially disruptive power to oversee the elected branches’ conduct of war. They left it to the U.S. District and Appeals Courts in the District of Columbia to make up detailed rules on an ad hoc basis.

This new regime of judicial second-guessing of military decisions now plagues President Obama as he wrestles with detainee-related problems that would be nightmarishly difficult even if he did not have to answer to the courts.

While dropping the label that Bush applied to most of these men — "enemy combatants" — the Obama Justice Department has adopted almost unchanged Bush’s residual claims of broad executive power to hold or transfer them without judicial interference. And although Obama applauded last June’s Supreme Court decision on the campaign trail, he now finds himself hemmed in by lower court rulings extending it.

On April 2, for example, Judge John Bates ruled that — contrary to Obama’s position — three non-Afghan prisoners who were moved to a U.S. military prison at Bagram Air Base in Afghanistan after being captured in other countries were entitled to judicial review of their petitions for release.

Meanwhile, the Obama Justice Department has embraced Bush’s appeals of two other District Court rulings, both in favor of 17 Chinese Muslims — members of the Uighur ethnic minority — at Guantanamo. One judge ordered the men released into the United States in light of the government’s admissions that they are not dangerous to Americans, might face torture if returned to China, and have not been offered refuge elsewhere. Another decision barred the government from transferring the Uighurs to any other country without 30 days notice to allow their lawyers to seek judicial relief. The government has won both appeals, but lawyers for the Uighurs petitioned the Supreme Court on April 6 to reinstate the order that they be released.

The squadrons of liberal lawyers who have flocked to the suspected terrorists’ defense have also filed more than 200 other habeas petitions and lawsuits, among them claims seeking redress for suspected abuses including torture and a petition to hold Defense Secretary Robert Gates in contempt of court.

The potential for disruptive and even dangerous judicial intrusions into military matters is considerable.

So clogged with detainee cases are the federal courts in D.C. that they may not have time to conduct any ordinary civil trials this spring or summer. So unclear is the law that conflicting rulings are inevitable. And the potential for disruptive and even dangerous judicial intrusions into military matters is considerable.

Will all U.S. prisoners, in every corner of the globe, be entitled to judicial process? Must suspected jihadi terrorists be given their Miranda rights — to remain silent, to consult lawyers, and all that — the minute they are securely in custody? Must they be released, no matter how dangerous they may be, unless the government can prove beyond a reasonable doubt that they have committed crimes? Or unless it can prove that they were fighting for Al Qaeda or the Taliban on a traditional battlefield, to the satisfaction of federal judges thousands of miles from the war zone, under the exacting evidentiary rules used in ordinary criminal cases? Must sensitive intelligence secrets be shared with the detainees or their lawyers? How long can the military hold those who are shown to be enemy fighters?

And might the courts start second-guessing other military decisions, such as the targeting of suspected terrorists in Pakistan for missile attacks? Will lawsuits by widows who say that their innocent husbands were recklessly blown to bits by U.S. missiles follow in the wake of the claims by former detainees who say they were tortured?

One can search the opinions of the Supreme Court in vain for clear guidance on how such questions should be answered. Instead, the justices have provided only "a set of shapeless procedures to be defined by federal courts at some future date," in the words of a June 2008 dissent by Chief Justice John Roberts.

Fortunately, the lower courts have so far handled these cases sensibly, in hundreds of pages of complex opinions. Judge Bates’s April 2 ruling for the three Bagram detainees, for example, strikes a careful balance that could provide Obama with a road map for minimizing judicial intervention by improving the military’s own process for determining who should be detained.

Bates, a Bush appointee, stressed that the three men (two Yemenis and a Tunisian) whose petitions he will review were apprehended in other countries and brought to the Bagram prison over six years ago. He reasoned that, as the Supreme Court held last June in the context of Guantanamo, the executive should not be free to "move detainees physically beyond the reach of the Constitution and detain them indefinitely."

But Judge Bates also emphasized that Bagram, unlike Guantanamo, is in an active theater of war and "under constant threat by suicide bombers and other violent elements." He therefore stopped well short of asserting judicial power to review military detentions of the vast majority of Bagram’s 600 prisoners — those who were captured on Afghan battlefields or are Afghan citizens.

The judge further emphasized that the military’s rudimentary process for hearing claims by Bagram prisoners that they are innocent noncombatants is even "less sophisticated and more error-prone" than the Guantanamo "combatant status review tribunals" that the Supreme Court found to be deficient. The president could "forestall judicial superintendence of the military’s detention policies," Bates suggested, by adopting a more fair and reliable military process.

Another way for Obama to inspire judicial deference, and to avoid a Supreme Court order releasing the Uighurs into the U.S., which could lead in turn to court-ordered release of more-dangerous detainees, would be to free the Uighurs himself, as a matter of simple fairness. This would not only moot the legal case but also increase the likelihood that other nations will take in some of the more than 40 other Guantanamo detainees whom the Pentagon has classified as nondangerous.

For the long run, the best way to avoid undue judicial interference and minimize the possibility of court-ordered release of truly dangerous detainees would be for Obama to seek legislation carefully defining how close a link to Al Qaeda or the Taliban must be proved to justify detaining a suspect; specifying procedural rules flexible enough to admit all reliable evidence while protecting classified information; requiring periodic reviews to identify detainees who may no longer be dangerous; and creating a new national security court with special expertise to review detainees’ appeals.

Meanwhile, the courts should balance their commendable zeal to prevent arbitrary executive detentions with an appreciation of the two dangers of forcing the release of men who may be terrorists. The first is the possibility that they will end up killing our troops or civilians. The second is the risk of sending our troops the unintended message that the safest course is to take no prisoners.

This article appeared in the Saturday, April 11, 2009 edition of National Journal.