The CIA says it believed it was operating lawfully in detaining and interrogating 96 suspected terrorists at locations from Thailand to Europe, until the US Supreme Court this summer demolished that legal foundation.
The CIA is now squarely in the middle of election-year politics as the US Congress tries to write new definitions that could reshape the intelligence agency's program.
"At the end of the day, the director -- any director -- of the CIA must be confident that what he has asked an agency officer to do under this program is lawful," CIA Director Michael Hayden wrote employees on Thursday.
President George W. Bush was more blunt: "They don't want to be tried as war criminals," he said at a news conference on Friday.
The high court's ruling in June, in a case involving Salim Ahmed Hamdan, essentially said that the Geneva Conventions on the rights of wartime prisoners should apply to the suspected terrorists in CIA custody.
That meant that for the first time since the interrogation program was born in 2002, the Justice Department could not give the CIA a written opinion on whether its techniques still were legal.
Spy agencies rely on such opinions to justify activities that get little, if any, public scrutiny.
To Bush, the CIA and their allies, the law urgently needs to be changed to protect the interrogation program, which they consider one of the most important ways to deter attacks against the US.
"The Hamdan decision in effect calls a time-out in the war on terror," Republican Senate Majority Whip Mitch McConnell said.
But the program's detractors say a fix is needed to prevent further damage to the US image abroad and to reduce risks to US military personnel who may be caught by enemies.
"The world is beginning to doubt the moral basis of our fight against terrorism," retired General Colin Powell, the former secretary of state, wrote Senator John McCain. The Arizona Republican is resisting Bush's call for more lenient rules on interrogations.
The CIA's practices raised concerns almost from the day that the agency began questioning detainees suspected of terrorist links.
Early in the US invasion of Afghanistan in 2001, senior military officers were so concerned about the CIA's practices that they took steps to ensure that military personnel were not in the room during CIA interrogations, said a government official familiar with both military and intelligence operations. The official and others in government and on Capitol Hill spoke recently about the sensitive CIA activities on the condition they not be identified.
But Gary Berntsen, the commander of a CIA team in Afghanistan in the fall of 2001, said CIA personnel initially did not have time for interrogations -- a term from the military and intelligence world that implies the use of specific techniques to coerce information from prisoners.
Instead, he said, intelligence officers conducted cursory interviews of newly captured fighters to see if they had information they wanted to share.
"We were seizing one city after the next," Berntsen commented. "There were hundreds of people" in custody.
He credits a British team in Afghanistan with obtaining a tip in Dec. 2001 on the details of a Singapore plot to use 21 tons of explosives to try to blow up the US, British, Israeli and Australian embassies in a follow-up attack to the Sept. 11 attacks. "We were desperate to find the next attack," Berntsen said.
Not long after the March 2002 capture of top al-Qaeda operative Abu Zubaydah, the CIA's practices became more formal. Agency operatives knew Zubaydah had a wealth of information because of his role as a recruiter and his close ties to al-Qaeda's senior leadership, but he was not cooperative.
The CIA decided it would need to hold high-value terrorists such as Zubaydah for extended periods in an effort to extract information. They also began successfully using some "enhanced interrogation techniques."
One senior US official says "only a fraction" of the agency's 96 high-value detainees have experienced those techniques because "the least obtrusive means are used."
Yet by mid-2004, the CIA's inspector general had completed a report on the treatment of detainees after the possible involvement of CIA personnel in the deaths of at least four prisoners. The review covered interrogation tactics.
Current and former US officials say some techniques are well-known: exposing prisoners to cold, disorienting them or depriving them of sleep. The most controversial is known as "waterboarding," when a detainee is strapped to a board and has water run over him to simulate drowning.
Bush administration officials say the Justice Department has deemed the CIA's practices lawful. In addition, the senior US official said the House and Senate Intelligence committees have now been told everything about the CIA's overseas prisons and interrogation program, except the countries where the prisons were located.
But a congressional aide disputed that. The aide said that briefings for the Senate committee took place only recently and that the administration has denied the committee access to materials it needs to fulfill its oversight role of the CIA.
For example, the committee's top Democrat, Senator Jay Rockefeller, has not been able to see the Justice Department's legal opinions.
The Supreme Court's decision froze the interrogations and led the administration to turn over the last 14 prisoners in CIA custody to the military officials running a prison for detainees at Guantanamo Bay, Cuba.
The next step is up to Congress. Lawmakers are struggling over how to write legislation creating rules for how to try suspected terrorists and how to specify the lengths that authorities can go in questioning these detainees.
A bill favored by McCain and two other influential Republican senators would prevent CIA personnel involved in the detention program from being sued or prosecuted for their actions. The CIA wants the Congress to go one step further and bless its actions.
In his memo to CIA personnel last week, Hayden also said he wants Congress to define, in US law, the terms of the Geneva Conventions that bar "humiliating and degrading treatment" and "outrages upon personal dignity."
Human rights groups see the effort as an end run and contend that established military rules could be applied to all government agencies, including the CIA.
"The only point in having a CIA program is to use techniques that go well beyond what is permitted by the Army Field Manual," said Tom Malinowski, Washington director for Human Rights Watch.
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