A few days after terrorists toppled the World Trade Center in 2001, Vice President Dick Cheney said the U.S. would have to "work ... the dark side" in order to destroy Osama bin Laden's network. Just what the dark side could mean became clearer last month when George Bush suddenly announced that 14 suspected al-Qaeda terrorists had been shipped from mysterious overseas locations to the U.S. detention center at Guantánamo Bay, Cuba. It was the first White House confirmation of a secret CIA-operated network of overseas prisons, places where unorthodox methods of interrogation were not unknown. "Were it not for this program," Bush said, referring to the secret prisons and the things done there, "al-Qaeda and its allies would have succeeded in launching another attack against the American homeland."

When Congress adopted legislation last week to establish military commissions to try terrorist suspects, it also gave approval to that program and then some. By allowing coerced testimony to be entered as evidence in trials, Congress potentially legitimized torture as a means of obtaining information. It left the President in charge of filling in the details of what the allowable methods should be. The clearest limit to what might be done was actually not so clear. The new methods could not constitute "grave breaches" of the Geneva Conventions. But after all the huffing and puffing from Republican Senators John McCain, John Warner and Lindsey Graham, the Executive Branch kept control over what exactly could happen to an "enemy combatant." It was allowed to decide who an enemy combatant might be. The package of measures widened the definition to include any person determined to be one under criteria defined by the President or the Secretary of Defense.

More than that, the measures adopted by Congress last week stripped defendants of the ancient habeas corpus right to challenge their detention in court--a step that makes it possible that the Supreme Court will strike down some portion of the law and send everybody back to the drawing board. "The Supreme Court has made clear on three recent occasions that those whom the White House labels enemy combatants are entitled to challenge their detention before a federal judge," says Eric Freedman, a law professor at Hofstra University who is a legal consultant to Guantánamo detainees. "This new law was passed in outright defiance of those rulings."

What the legislation is likely to do even sooner is put the CIA's secret-prison program back online. That's right: back online. Although when he revealed its existence, the President left the impression he had suspended the program in response to a June Supreme Court ruling, that's not so. What neither he nor Congress nor the CIA has publicly acknowledged is that the agency halted the "special interrogations" in its secret prisons more than nine months ago. People briefed on the matter tell TIME that the agency backed away from its program in December 2005 as Congress passed an amendment to the 2006 defense bill banning "cruel, inhuman or degrading" treatment of prisoners in U.S. custody. According to other U.S. officials, then CIA Director Porter Goss feared that the amendment, sponsored by McCain, might undercut the legal authority for CIA interrogations. So Goss put those procedures on hold while seeking a legal opinion from the Justice Department.

For the next nine months, says a person briefed on activity in the program, some at the agency developed a bias for killing its targets instead of bringing them in for questioning, though sources add that ground conditions make capture impossible anyway. Goss's suspension order left officers in the agency's directorate of operations, says the source, repeatedly asking the question, What are we going to do with these guys if we capture them? So far in 2006, as government sources and public reports indicate, few if any terrorist suspects have been captured by the CIA. But at least four--including bombmaker Abu Khabab al- Masri, on the FBI's most-wanted list--have been killed, in most cases by remotely fired missiles from Predator drones.

The rules adopted last week may mean a return to the practice of capture and question. But question how? Just what interrogation methods are off the table now? Depends on whom you talk to. McCain, who along with Graham and Warner had fought the Administration on some of the most coercive methods, insisted to reporters last week that the harshest techniques--such as waterboarding, stress positions, extreme sleep deprivation and hypothermia--could now be illegal. "For all the gloating from the Administration," says Tom Malinowski of Human Rights Watch, "they are not getting what they want on torture." And what methods are O.K.? No one inside or outside the CIA will say. Which may mean we're going to be fighting on "the dark side" for some time to come.
With reporting by Timothy J. Burger, Massimo Calabresi, Adam Zagorin/Washington

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