According to a CNN interview with intelligence expert Rohan Gunaratna, "Daniel Pearl was going in search of the al Qaeda network that was operational in Karachi, and it was at the instruction of Khalid Sheikh Mohammed that Daniel Pearl was killed." On October 12, 2006, Time magazine reported that "KSM confessed under CIA interrogation that he personally committed the murder." On March 15, 2007, the Pentagon stated that Mohammed had confessed to the murder. The statement quoted Mohammed as saying, "I decapitated with my blessed right hand the head of the American Jew, Daniel Pearl, in the city of Karachi, Pakistan. For those who would like to confirm, there are pictures of me on the Internet holding his head." This confession was gained under torture, and Mohammed listed many other crimes at the same time.
In September 2006, the U.S. government announced it had moved Mohammed from a secret CIA prison (or black site) to the military custody at the Guantanamo Bay detention camp.
In October 2006, Mohammed described his mistreatment and torture in detention, including the waterboarding, to a representative of the International Committee of the Red Cross. Mohammed said that he had provided a lot of false information, which he had supposed the interrogators wanted to hear, in order to stop the mistreatment. In the 2006 interview with the Red Cross, Mohammed claimed to have been waterboarded in five different sessions during the first month of interrogation in his third place of detention. While the Justice Department memos did not explain exactly what the numbers represented, a U.S. official with knowledge of the interrogation programs explained the 183 figure represented the number of times water was applied to the detainee's face during the waterboarding sessions, rather than separate sessions.
Ali Khan, the father of Majid Khan, another one of the 14 "high-value detainees," released an affidavit on April 16, 2006, that reported that interrogators subjected Khalid Sheikh Mohammed's children, aged 6 and 8 years old, to abusive interrogation.
On September 6, 2006, then-American President George W. Bush confirmed, for the first time, that the CIA had held "high-value detainees" for interrogation in secret prisons around the world. He also announced that fourteen senior captives, including Khalid Sheikh Mohammed, were being transferred from CIA custody, to military custody, at Guantanamo Bay detention camp and that these fourteen captives could now expect to face charges before Guantanamo military commissions.
"In 2006, his interrogation summaries were read aloud in the capital murder trial of Zacarias Moussaoui, the so-called 20th hijacker, and Moussaoui was spared the death penalty. Two years later, different Mohammed statements were read in a military commission trial, or tribunal, that led to the release from Guantanamo Bay of Osama bin Laden's chauffeur, Salim Hamdan."