This column originally appeared in Townhall.com on April 20, 2009.

Recently, a federal court issued a decision that may be the next Supreme Court case in the War on Terror. The court ruled that terrorists held by the U.S. military in Afghanistan are entitled to the writ of habeas corpus, extending a panoply of rights to these detainees. This ruling could have a stunning impact on this and future wars, and bears out just how wrong last year’s major Supreme Court habeas case was.

Judge John D. Bates is a Bush appointee on the U.S. District Court for the District of Columbia. Judge Bates held that terrorist detainees that are held at the Bagram Air Force Base are entitled to habeas corpus, claiming that the Supreme Court’s 2008 decision in Boumediene v. Bush demands this result.

The writ of habeas corpus is powerful. Where habeas applies, it requires that any person held in confinement must either be promptly given a civilian trial with all the protections that the Bill of Rights gives American citizens, or that the person must be released. Before the Boumediene case, it had never been applied in a wartime context on foreign soil in the history of the United States.

No country extends more protections for individual liberty than the United States. Our nation has amazingly broad protections for free speech, religious liberty and political expression. People have the right to own property, have the means to defend themselves and their families, and be informed by a free press. If the government wants to convict them, they are presumed innocent, entitled to a prompt jury trial with the help of a lawyer, and cannot be tortured or given unreasonable fines.

Yet before last year, the courts always recognized the enormous difference between prosecuting criminals and fighting a war. Habeas corpus applies to American citizens or people on American soil as part of domestic policy. When invoked, it requires the government to apply all of those rights listed above. It’s a civilian process deliberately biased in favor of defendants that is focused on our courts under Article III of the Constitution.

War, on the other hand, is a military matter. It’s part of foreign policy under the president’s commander-in-chief power in Article II of the Constitution. It’s deliberately biased in favor of American power, intended to protect American lives and our national security.

Then Boumediene v. Bush came along, striking down the military commission system in Guantanamo Bay, Cuba (Gitmo). For the first time, with a 5-4 split decision, the Article III branch chose to override the Article I Congress that created the military commission system and the Article II president who was fighting a war. The four conservative justices that dissented in that case warned that America would regret the majority’s decision.

Today may be the beginning of that regret. Habeas here means everyone captured on battlefields is presumed innocent and gets taxpayer-funded defense lawyers and every right of Americans. That includes making the soldiers involved to be flown back to the U.S. for the terrorist’s trial, where they’ll have to testify and defend themselves. The soldiers will have to provide evidence to prove their allegations about the terrorist defendant. If they can’t prove every part of what they say, the terrorist will go free.

What’s surprising about this decision is that it wasn’t necessary. Judge Bates wrote that habeas had to apply in Afghanistan because Bagram Air Force Base could not be distinguished from Gitmo.

That’s just not so. In Johnson v. Eisentrager in 1950, the Court held that habeas did not apply to the U.S. military bases in Germany. In Boumediene, the Court bent over backwards to explain why Gitmo was different from Germany, saying that Gitmo was a century-long lease from Cuba that amounted to complete and permanent U.S. control. Therefore, Boumediene held, Gitmo was de facto sovereign American soil, and that’s why habeas applies.

U.S. bases in Afghanistan are more like those in Germany than Cuba. Bagram Air Force Base is just like the bases in Germany after World War II. If habeas didn’t apply to Germany in the Eisentrager case, then it shouldn’t apply in Afghanistan.

Judge Bates is considered a conservative judge with an excellent reputation. It could be that he felt compelled by the Boumediene case, which he must follow even if he disagrees with it. But this decision seems to go further than the case required, and will now be appealed to the D.C. Circuit. This case could go all the way to the Supreme Court, and change the way America conducts wars forever.