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Was there a covert CIA prison system?

        Science | Soldiers

Black Sites
In a 2006 visit to Atlanta, President George W. Bush (with Georgia Gov. Sonny Perdue) affirmed the existence of secret prisons.
In a 2006 visit to Atlanta, President George W. Bush (with Georgia Gov. Sonny Perdue) affirmed the existence of secret prisons.
Jim Watson/AFP/Getty Images

The first black site established by the CIA following the Sept. 11 attacks was located in Thailand. Its first detainee was a top al-Qaida operative, Abu Zubaydah, who was captured in a shoot-out in Pakistan. Zubuydah suffered a gunshot wound and was treated for his injury. Following his recovery, he was subjected to interrogation methods considered torture under U.S. and international law (such as beatings, long periods of standing and water boarding). But he was also reported to have been treated well. Zubuydah was fed breakfast, lunch and dinner, including baked chicken and candy bars -- specifically, Kit-Kats [source: ABC News].

Zubaydah was soon joined by fellow al-Qaida members, including Khalid Sheik Mohammed, the alleged mastermind behind the Sept. 11 attacks [source: BBC]. But accusations that the United States was illegally detaining terror suspects at secret prisons in Thailand caused the Thai government to close the CIA-run facility in 2003. The following year, another black site at the detention facility at Guantanamo Bay was closed [source: Washington Post].

But the CIA still had terror suspects on their hands. Other sites, located in Afghanistan, Romania and Poland were established. These black sites had code names like Salt Pit and Bright Light [source: Risen]. At these secret prisons, an investigation by the Council of Europe found that the CIA subjected detainees to enhanced interrogation techniques -- including water boarding [source: The Guardian]. In one case, a detainee held at a black site in Afghanistan froze to death under CIA supervision [source: Washington Post]. In another, nine of 10 suspects held at secret prisons in Romania and Poland were subjected to water boarding [source: ABC News].

The CIA divided terror suspects into two classifications: high value and lesser value. The high value targets were kept in the secret prisons. Lesser value targets were rendered to foreign countries or sent to Guantanamo Bay [source: Washington Post]. The CIA's secret prisons were reportedly established in collusion with the governments where the black sites were located. Only a handful of people in the American and foreign governments and intelligence agencies were aware the prisons existed [source: Washington Post].

The CIA's secret prison network still left a paper trail, however. Flight manifests clued in human rights groups investigating allegations of the existence of secret, CIA-operated prisons -- ultimately, they discovered the network. By tracing the movement of these flights and the stated nationalities of the passengers on the flights' manifests, human rights groups began to uncover the CIA's secret prison network. The CIA chartered airline flights and private planes to move the detainees. Other flights were conducted on planes registered to what turned out to be CIA dummy companies [source: Amnesty International].

One CIA-chartered flight was found to have departed Afghanistan and stopped in Poland, Romania and Morocco before arriving in Guantanamo Bay [source: Deutsche Welle]. Further investigation found that NATO-member countries had signed a waiver in 2001 that allowed private U.S. planes to fly in the nations' airspace [source: The Guardian].

In 2005, in the face of international pressure, the European black sites were closed. Inmates were transferred to another secret prison in North Africa [source: ABC News]. The following year, making the first official acknowledgement that the sites had ever existed, President George W. Bush announced that all of the secret prisons had been shut down and the detainees transferred to Guantanamo Bay. Bush justified the prisons, saying that suspects had not been tortured and that their secret detainment had helped saved lives [source: BBC].

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