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On the day of the attacks, the CIA already had a list of what it called High-Value Targets from the al Qaeda structure, and as the World Trade Center and Pentagon attack plots were unraveled, more names were added to the list. The question of what to do with these people surfaced quickly.
The CTC's chief of operations argued for creating hit teams of case officers and CIA paramilitaries that would covertly infiltrate countries in the Middle East, Africa and even Europe to assassinate people on the list, one by one.
But many CIA officers believed that the al Qaeda leaders would be worth keeping alive to interrogate about their network and other plots. Some officers worried that the CIA would not be very adept at assassination.
"We'd probably shoot ourselves," another former senior CIA official said.
The agency set up prisons under its covert action authority. Under U.S. law, only the president can authorize a covert action, by signing a document called a presidential finding. Findings must not break U.S. law and are reviewed and approved by CIA, Justice Department and White House legal advisers.
Six days after the Sept. 11 attacks, President Bush signed a sweeping finding that gave the CIA broad authorization to disrupt terrorist activity, including permission to kill, capture and detain members of al Qaeda anywhere in the world.
It could not be determined whether Bush approved a separate finding for the black-sites program, but the consensus among current and former intelligence and other government officials interviewed for this article is that he did not have to.
Rather, they believe that the CIA general counsel's office acted within the parameters of the Sept. 17 finding. The black-site program was approved by a small circle of White House and Justice Department lawyers and officials, according to several former and current U.S. government and intelligence officials.
Deals With 2 Countries
Among the first steps was to figure out where the CIA could secretly hold the captives. One early idea was to keep them on ships in international waters, but that was discarded for security and logistics reasons.
CIA officers also searched for a setting like Alcatraz Island. They considered the virtually unvisited islands in Lake Kariba in Zambia, which were edged with craggy cliffs and covered in woods. But poor sanitary conditions could easily lead to fatal diseases, they decided, and besides, they wondered, could the Zambians be trusted with such a secret?
Still without a long-term solution, the CIA began sending suspects it captured in the first month or so after Sept. 11 to its longtime partners, the intelligence services of Egypt and Jordan.
A month later, the CIA found itself with hundreds of prisoners who were captured on battlefields in Afghanistan. A short-term solution was improvised. The agency shoved its highest-value prisoners into metal shipping containers set up on a corner of the Bagram Air Base, which was surrounded with a triple perimeter of concertina-wire fencing. Most prisoners were left in the hands of the Northern Alliance, U.S.-supported opposition forces who were fighting the Taliban.
"I remember asking: What are we going to do with these people?" said a senior CIA officer. "I kept saying, where's the help? We've got to bring in some help. We can't be jailers -- our job is to find Osama."
Then came grisly reports, in the winter of 2001, that prisoners kept by allied Afghan generals in cargo containers had died of asphyxiation. The CIA asked Congress for, and was quickly granted, tens of millions of dollars to establish a larger, long-term system in Afghanistan, parts of which would be used for CIA prisoners.
The largest CIA prison in Afghanistan was code-named the Salt Pit. It was also the CIA's substation and was first housed in an old brick factory outside Kabul. In November 2002, an inexperienced CIA case officer allegedly ordered guards to strip naked an uncooperative young detainee, chain him to the concrete floor and leave him there overnight without blankets. He froze to death, according to four U.S. government officials. The CIA officer has not been charged in the death.
The Salt Pit was protected by surveillance cameras and tough Afghan guards, but the road leading to it was not safe to travel and the jail was eventually moved inside Bagram Air Base. It has since been relocated off the base.
By mid-2002, the CIA had worked out secret black-site deals with two countries, including Thailand and one Eastern European nation, current and former officials said. An estimated $100 million was tucked inside the classified annex of the first supplemental Afghanistan appropriation.
Then the CIA captured its first big detainee, in March 28, 2002. Pakistani forces took Abu Zubaida, al Qaeda's operations chief, into custody and the CIA whisked him to the new black site in Thailand, which included underground interrogation cells, said several former and current intelligence officials. Six months later, Sept. 11 planner Ramzi Binalshibh was also captured in Pakistan and flown to Thailand.
But after published reports revealed the existence of the site in June 2003, Thai officials insisted the CIA shut it down, and the two terrorists were moved elsewhere, according to former government officials involved in the matter. Work between the two countries on counterterrorism has been lukewarm ever since.
In late 2002 or early 2003, the CIA brokered deals with other countries to establish black-site prisons. One of these sites -- which sources said they believed to be the CIA's biggest facility now -- became particularly important when the agency realized it would have a growing number of prisoners and a shrinking number of prisons.
Thailand was closed, and sometime in 2004 the CIA decided it had to give up its small site at Guantanamo Bay. The CIA had planned to convert that into a state-of-the-art facility, operated independently of the military. The CIA pulled out when U.S. courts began to exercise greater control over the military detainees, and agency officials feared judges would soon extend the same type of supervision over their detainees.
In hindsight, say some former and current intelligence officials, the CIA's problems were exacerbated by another decision made within the Counterterrorist Center at Langley.
The CIA program's original scope was to hide and interrogate the two dozen or so al Qaeda leaders believed to be directly responsible for the Sept. 11 attacks, or who posed an imminent threat, or had knowledge of the larger al Qaeda network. But as the volume of leads pouring into the CTC from abroad increased, and the capacity of its paramilitary group to seize suspects grew, the CIA began apprehending more people whose intelligence value and links to terrorism were less certain, according to four current and former officials.
The original standard for consigning suspects to the invisible universe was lowered or ignored, they said. "They've got many, many more who don't reach any threshold," one intelligence official said.
Several former and current intelligence officials, as well as several other U.S. government officials with knowledge of the program, express frustration that the White House and the leaders of the intelligence community have not made it a priority to decide whether the secret internment program should continue in its current form, or be replaced by some other approach.
Meanwhile, the debate over the wisdom of the program continues among CIA officers, some of whom also argue that the secrecy surrounding the program is not sustainable.
"It's just a horrible burden," said the intelligence official.