By Cora Currier, ProPublica, Feb. 13, 2013

In one of President Barack Obama first acts in the White House, he ordered the closure of the CIA's so-called "black-site" prisons, where terror suspects had been held and, sometimes, tortured.  The CIA says it is "out of the detention business," as John Brennan, Obama's pick to head the agency, recently put it.

But the CIA's prisons left some unfinished business.  In 2009, ProPublica's Dafna Linzer listed more than thirty people who had been held in CIA prisons and were still missing.

Some of those prisoners have since resurfaced, but at least twenty are still unaccounted for.

Last week the Open Society Foundations' Justice Initiative released a report pulling together the most current information available on the fates of the prisoners. A few emerged from foreign prisons after the turmoil of the Arab Spring. One has died. (The report relied exclusively on media accounts and information previously gathered by human rights groups. The Open Society Foundations also donate to ProPublica.)

The report counts 136 prisoners who were either held in a CIA black site or subject to so-called extraordinary rendition, in which detainees were secretly shipped to other countries for interrogation.

Many of the prisoners were tortured, either under the CIA's "enhanced interrogation techniques" program or by other countries after their transfer. The report also lists 54 countries that assisted in some way with detention and rendition. The U.S. has not disclosed the countries it worked with, and few have acknowledged their participation.

The CIA declined our request to comment.

Here are the fates of a few of the prisoners we listed as missing back in 2009:

• Ayoub al-Libi, also known as Mustafa Jawda al-Mahdi, is a Libyan who was allegedly interrogated and detained by US personnel in Pakistan and Afghanistan in 2004. The next year he was returned to Libya, where he was sentenced to death as member of LIFG, an Islamist anti-Gaddafi group (designated a terrorist organization by the U.S.) He was released when uprisings began against Gaddafi in February 2011. Human Rights Watch interviewed him in 2012.

• Hassan Rabai, also known as Mohamed Ahmad Mohamed Al Shoroieya, is a Libyan who was captured in Pakistan in 2003 and later transferred to Afghanistan – where he alleges that he was waterboarded by U.S. personnel. Bush administration officials have repeatedly said that only three terror suspects were ever subjected to waterboarding; Rabai would be the fourth. He was eventually transferred to prison in Libya, where he remained until February 2011. Human Rights Watch interviewed him last year.

• Khaled al-Sharif, also known as Abu Hazam, was picked up with fellow Libyan and LIFG member Hassan Rabai and also held in Afghanistan. He remained in Libyan prison until March 2010, according to interviews he gave to Human Rights Watch.

• Mohammed Omar Abdel-Rahman is an Egyptian who was captured in Pakistan in 2003 and considered a “senior Al-Qaeda operative.” He was transferred to prison in Egypt and was released in late 2010. He gave an interview in 2011 in which he admitted to running training camps in Afghanistan prior to 2001 but saying he had renounced violence.

• Mustafa Setmariam Nasar, also known as Abu Musab al-Suri, was tied to the bombings in Madrid and London in 2004 and 2005. Picked up by the CIA in 2005, he was transferred to prison in his native Syria. According to Syrian media, he was released by Syrian president Bashar Al-Assad in February 2012.

• Ali Abdul-Hamid al-Fakhiri, also known as Ibn al-Sheikh al-Libi, was a Libyan detained shortly after the 9/11 attacks. He was reportedly held in CIA as well as Egyptian custody over the next several years. According to a Senate Intelligence Committee report, he provided information about links between Iraq’s supposed weapons of mass destruction and Al Qaeda – information he later said he had fabricated. He was transferred to Libyan prison in 2005 or 2006, and was found dead in his cell in May 2009.

The whereabouts (and in some cases identities) of many more remain unknown or uncertain.

In 2007, then-CIA director Michael Hayden said that “fewer than 100 people had been detained at CIA’s facilities.” But only 16 have been officially identified by the U.S. government. President George W. Bush acknowledged the CIA’s detention program in September 2006 and announced the transfer of 14 “high-value” detainees to Guantanamo Bay prison. Two other high-value detainees were subsequently acknowledged.

Much else about the CIA program is still unknown. President Barack Obama closed the black-site prisons on entering office, but preserved the ability to render and to hold people for the “short-term.”

Obama banned torture, but announced that no one would be prosecuted for previously sanctioned harsh interrogations. A Justice Department investigation into deaths of detainees in CIA custody ended without charges.

The Senate Intelligence Committee recently completed a 6,000-page report on the CIA’s detention program. At Brenan’s confirmation hearings, Senator Jay Rockefeller (D-W.V.), said the report shows the interrogation program was run by people “ignorant of the topic, executed by personnel without relevant experience, managed incompetently by senior officials who did not pay attention to detail, and corrupted by personnel with pecuniary conflicts of interest.” Rockefeller is one of the few to have read the report, which remains classified.