In August 2004 Pakistani officials stated that al-Libbi had become "number three" in al-Qaeda as "director of operations", a role once filled by Khalid Sheikh Mohammed.
Upon al-Libbi's arrest on May 2, 2005, U.S. and Pakistani authorities continued to claim him as the third most important figure in al-Qaeda. According to the BBC and Voice of America (VOA) reports, he was riding pillion on a motorbike when he and his driver were ambushed by Pakistani agents, some of whom were wearing burqas. A VOA reporter from Mardan said that while being apprehended, al-Libbi tried to destroy a notebook, which U.S. agents took and have tried to decode.
US agents had been trying to find al-Libbi as a link to finding Osama bin Laden. After they intercepted a mobile phone call made by him, they targeted his location to a busy road a quarter of a mile away on the outskirts of Mardan, about 75 mi (121 km) northwest of Islamabad, and tipped-off Pakistani authorities. Plainclothes Pakistani agents arrived in Mardan and waited for him to arrive.
In the early reporting of this capture, there was confusion between the names and identities of Abu Faraj al-Libbi and another wanted al-Qaeda fugitive, Anas al-Liby.Al-Libi is not a surname, but an adjective, meaning the Libyan. Such adjectives of nationality are used in nicknames, and sometimes to resolve ambiguity; they often have several alternative English transliterations.
When he assumed office in January 2009 PresidentBarack Obama made a number of promises about the future of Guantanamo. He promised the use of torture would cease at the camp. He promised to institute a new review system. That new review system was composed of officials from six departments, where the OARDEC reviews were conducted entirely by the Department of Defense. When it reported back, a year later, the Joint Review Task Force classified some individuals as too dangerous to be transferred from Guantanamo, even though there was no evidence to justify laying charges against them. On April 9, 2013, that document was made public after a Freedom of Information Act request. Mustafa Faraj Muhammad Masud al-Jadid al-Uzaybi was one of the 71 individuals deemed too innocent to charge, but too dangerous to release. Although Obama promised that those deemed too innocent to charge, but too dangerous to release would start to receive reviews from a Periodic Review Board less than a quarter of men have received a review.