In late 2002 or early 2003

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.