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According to the ICRC, some of the prisoners were bounced around to different black sites for more than three years, where they were kept in “continuous solitary confinement and incommunicado detention. They had no knowledge of where they were being held, no contact with persons other than their interrogators or guards.” The US personnel guarding them wore masks. None of the prisoners was ever permitted a phone call or to write to inform their families they had been taken. They simply vanished.

During the course of their imprisonment, some of the prisoners were confined in boxes and subjected to prolonged nudity—sometimes lasting for several months. Some of them were kept for days at a time, naked, in “stress standing positions,” with their “arms extended and chained above the head.” During this torture, they were not allowed to use a toilet and “had to defecate and urinate over themselves.” Beatings and kickings were common, as was a practice of placing a collar around a prisoner’s neck and using it to slam him against walls or yank him down hallways. Loud music was used for sleep deprivation, as was temperature manipulation. If prisoners were perceived to be cooperating, they were given clothes to wear. If they were deemed uncooperative, they’d be stripped naked. Dietary manipulation was used—at times the prisoners were put on liquid-only diets for weeks at a time. Three of the prisoners told the ICRC they had been waterboarded. Some of them were moved to as many as ten different sites during their imprisonment. “I was told during this period that I was one of the first to receive these interrogation techniques, so no rules applied,” one prisoner, taken early on in the war on terror, told the ICRC. “I felt like they were experimenting and trying out techniques to be used later on other people.”

And:

While TF-121 was given a mission to kill or capture Osama bin Laden and Saddam Hussein by the spring of 2004, Washington was increasingly focused on Iraq. Veteran intelligence officials identify this period as a turning point in the hunt for bin Laden. At a time when JSOC was asking for more resources and permissions to pursue targets inside of Pakistan and other countries, there was a tectonic shift toward making Iraq the numberone priority.

The heavy costs of that strategic redirection to the larger counterterrorism mission were of deep concern to Lieutenant Colonel Anthony Shaffer, a senior military intelligence officer who was CIA trained and had worked for the DIA and JSOC. Shaffer ran a task force, Stratus Ivy, that was part of a program started in the late 1990s code-named Able Danger. Utilizing what was then cutting-edge “data mining” technology, the program was operated by military intelligence and the Special Operations Command and aimed at identifying al Qaeda cells globally. Shaffer and some of his Able Danger colleagues claimed that they had uncovered several of the 9/11 hijackers a year before the attacks but that no action was taken against them. He told the 9/11 Commission he felt frustrated when the program was shut down and believed it was one of the few effective tools the United States had in the fight against al Qaeda pre-9/11. After the attacks, Shaffer volunteered for active duty and became the commander of the DIA’s Operating Base Alpha, which Shaffer said “conducted clandestine antiterrorist operations” in Africa. Shaffer was running the secret program, targeting al Qaeda figures who might flee Afghanistan and seek shelter in Somalia, Liberia and other African nations. It “was the first DIA covert action of the post–Cold War era, where my officers used an African national military proxy to hunt down and kill al Qaeda terrorists,” Shaffer recalled.

Like many other experienced intelligence officers who had been tracking al Qaeda prior to 9/11, Shaffer believed that the focus was finally placed correctly on destroying the terror network and killing or capturing its leaders. But then all resources were repurposed for the Iraq invasion. “I saw the Bush administration lunacy up close and personal,” Shaffer said. After a year and a half of running the African ops, “I was forced to shut down Operating Base Alpha so that its resources could be used for the Iraq invasion.”

Shaffer was reassigned as an intelligence planner on the DIA team that helped feed information on possible Iraqi WMD sites to the advance JSOC teams that covertly entered Iraq ahead of the invasion. “It yielded nothing,” he alleged. “As we now know, no WMD were ever found.” He believed that shifting the focus and resources to Iraq was a grave error that allowed bin Laden to continue operating for nearly another decade. Shaffer was eventually sent to Afghanistan, where he would clash with US military leaders over his proposals to run operations into Pakistan to target the al Qaeda leaders who were hiding there.

And:

The task force’s operations, Exum said, were “very compartmentalized, very stove-piped.” JSOC was creating a system where its intelligence operations were feeding its action and often that intelligence would not be vetted by anyone outside of the JSOC structure. The priority was to keep hitting targets. “The most serious thing is the abuse of power that that allows you to do,” said Wilkerson, the former chief of staff to Powell. He continued: "You go in and you get some intelligence, and usually your intelligence comes through this apparatus too, and so you say, ‘Oh, this is really good actionable intelligence. Here’s Operation Blue Thunder. Go do it.’ And they go do it, and they kill 27, 30, 40 people, whatever, and they capture seven or eight. Then you find out that the intelligence was bad and you killed a bunch of innocent people and you have a bunch of innocent people on your hands, so you stuff ’em in Guantánamo. No one ever knows anything about that. You don’t have to prove to anyone that you did right. You did it all in secret, so you just go to the next operation. You say, ‘Chalk that one up to experience,’ and you go to the next operation. And, believe me, that happened."

More (#1) from Dirty Wars:

However, just as the FBI believed it was making headway with Libi, CIA operatives, on orders from Cofer Black, showed up at Bagram and demanded to take him into their custody. The FBI agents objected to the CIA taking him, but the White House overruled them. “You know where you are going,” one of the CIA operatives told Libi as he took him from the FBI. “Before you get there, I am going to find your mother and fuck her.”

The CIA flew Libi to the USS Bataan in the Arabian Sea, which was also housing the so-called American Taliban, John Walker Lindh, who had been picked up in Afghanistan, and other foreign fighters. From there, Libi was transferred to Egypt, where he was tortured by Egyptian agents. Libi’s interrogation focused on a goal that would become a centerpiece of the rendition and torture program: proving an Iraq connection to 9/11. Once he was in CIA custody, interrogators pummeled Libi with questions attempting to link the attacks and al Qaeda to Iraq. Even after the interrogators working Libi over had reported that they had broken him and that he was “compliant,” Cheney’s office directly intervened and ordered that he continue to be subjected to enhanced interrogation techniques. “After real macho interrogation—this is enhanced interrogation techniques on steroids—he admitted that al Qaeda and Saddam were working together. He admitted that al Qaeda and Saddam were working together on WMDs,” former senior FBI interrogator Ali Soufan told PBS’s Frontline. But the Defense Intelligence Agency (DIA) cast serious doubt on Libi’s claims at the time, observing in a classified intelligence report that he “lacks specific details” on alleged Iraqi involvement, asserting that it was “likely this individual is intentionally misleading” his interrogators. Noting that he had been “undergoing debriefs for several weeks,” the DIA analysis concluded Libi may have been “describing scenarios to the debriefers that he knows will retain their interest.” Despite such doubts, Libi’s “confession” would later be given to Secretary of State Powell when he made the administration’s fraudulent case at the United Nations for the Iraq War. In that speech Powell would say, “I can trace the story of a senior terrorist operative telling how Iraq provided training in these weapons to al Qaeda.” Later, after these claims were proven false, Libi, according to Soufan, admitted he had lied. “I gave you what you want[ed] to hear,” he said. “I want[ed] the torture to stop. I gave you anything you want[ed] to hear.”

And:

Although part of Rumsfeld’s visit to Fort Bragg was public, he was also there for a secret meeting—with the forces whose units were seldom mentioned in the press and whose operations were entirely shrouded in secrecy: the Joint Special Operations Command, or JSOC. On paper, JSOC appeared to be an almost academic entity, and its official mission was described in bland, bureaucratic terms. Officially, JSOC was the “joint headquarters designed to study special operations requirements and techniques; ensure interoperability and equipment standardization; plan and conduct joint special operations exercises and training; and develop joint special operations tactics.” In reality, JSOC was the most closely guarded secret force in the US national security apparatus. Its members were known within the covert ops community as ninjas, “snake eaters,” or, simply, operators. Of all of the military forces available to the president of the United States, none was as elite as JSOC. When a president of the United States wanted to conduct an operation in total secrecy, away from the prying eyes of Congress, the best bet was not the CIA, but rather JSOC. “Who’s getting ready to deploy?” Rumsfeld asked when he addressed the special operators. The generals pointed to the men on standby. “Good for you. Where you off to? Ahh, you’d have to shoot me if you told me, right?” Rumsfeld joked. “Just checking.”

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Colonel Lang said Bush “was so taken with President Saleh as a personable, friendly, chummy kind of guy, that Bush was in fact quite willing to listen to whatever Saleh said about, ‘We like you Americans, we want to help you, we want to cooperate with you,’ that kind of business, and was quite willing to send them foreign aid, including military aid.” During his meeting with President Bush in November 2001, Saleh “expressed his concern and hope that the military action in Afghanistan does not exceed its borders and spread to other parts of the Middle East, igniting further instability in the region,” according to a statement issued by the Yemeni Embassy in Washington at the end of the visit. But to keep Yemen off Washington’s target list, Saleh would have to take action. Or at least give the appearance of doing so.

Saleh’s entourage was given a list of several al Qaeda suspects that the Yemeni regime could target as a show of good faith. The next month, Saleh ordered his forces to raid a village in Marib Province, where Abu Ali al Harithi, a lead suspect in the Cole bombing, and other militants were believed to be residing. The operation by Yemeni special forces was a categorical failure. Local tribesmen took several of the soldiers hostage and the targets of the raid allegedly escaped unharmed. The soldiers were later released through tribal mediators, but the action angered the tribes and served as a warning to Saleh to stay out of Marib. It was the beginning of what would be a complex and dangerous chess match for Saleh as he made his first moves to satisfy Washington’s desire for targeted killing in Yemen while maintaining his own hold on power.

And:

In early July 2002, CIA interrogators began receiving training from SERE instructors and psychologists on extreme interrogation tactics. Later that month, Rumsfeld’s office requested documents from JPRA, “including excerpts from SERE instructor lesson plans, a list of physical and psychological pressures used in SERE resistance training, and a memo from a SERE psychologist assessing the long-term psychological effects of SERE resistance training on students and the effects of waterboarding,” according to a Senate Armed Services Committee investigation. “The list of SERE techniques included such methods as sensory deprivation, sleep disruption, stress positions, waterboarding, and slapping. It also made reference to a section of the JPRA instructor manual that discusses ‘coercive pressures,’ such as keeping the lights on at all times, and treating a person like an animal.” The Pentagon’s deputy general counsel for intelligence, Richard Shiffrin, acknowledged that the Pentagon wanted the documents in order to “reverse-engineer” SERE’s knowledge of enemy torture tactics for use against US detainees. He also described how JPRA provided interrogators with documents about “mind-control experiments” used on US prisoners by North Korean agents. “It was real ‘Manchurian Candidate’ stuff,” Shiffrin said. JPRA’s commander also sent the same information to the CIA.

The use of these new techniques was discussed at the National Security Council, including at meetings attended by Rumsfeld and Condoleezza Rice. By the summer of 2002, the War Council legal team, led by Cheney’s consigliere, David Addington, had developed a legal rationale for redefining torture so narrowly that virtually any tactic that did not result in death was fair game. “For an act to constitute torture as defined in [the federal torture statute], it must inflict pain that is difficult to endure. Physical pain amounting to torture must be equivalent in intensity to the pain accompanying serious physical injury, such as organ failure, impairment of bodily function, or even death,” Assistant Attorney General for the Office of Legal Counsel Jay Bybee asserted in what would become an infamous legal memo rationalizing the torture of US prisoners. “For purely mental pain or suffering to amount to torture under [the federal torture statute], it must result in significant psychological harm of significant duration, e.g., lasting for months or even years.” A second memo signed by Bybee gave legal justification for using a specific series of “enhanced interrogation techniques,” including waterboarding. “There was not gonna be any deniability,” said the CIA’s Rodriguez, who was coordinating the interrogation of prisoners at the black sites. “In August of 2002, I felt I had all the authorities that I needed, all the approvals that I needed. The atmosphere in the country was different. Everybody wanted us to save American lives.” He added, “We went to the border of legality. We went to the border, but that was within legal bounds.”