The Obama administration announced April 27 that CIA director Leon Panetta is to become defense secretary, replacing the retiring Robert Gates (himself a former CIA director), while the new CIA director will be Gen. David Petraeus, currently US commander in Afghanistan and formerly the architect of the Iraq "surge" as chief of Central Command. Analyzes the New York Times:

WikiLeaks on April 24 began publishing "The Guantanamo Files," a collection of more than 700 classified documents relating to the evidence against and treatment of almost all detainees held at Guantánamo Bay between 2002 and 2008. The documents—detailing things such as the circumstances of detention, the evidence justifying detention, detainee risk evaluations, and the decision process of which detainees to transfer, hold, or release of 758 of the 779 total detainees—were published in part on the WikiLeaks website and released to media outlets. According to the media outlets that have analyzed the documents, they reveal that 220 "high value" al-Qaeda operatives had been held at Guantánamo, in addition to 150 who had been held for years without significant evidence against them. The documents also detailed the practice of US forces detaining people in Afghanistan based on their wearing a particular model of watch that is known to be used by al-Qaeda leaders. Additionally, 20 juveniles were held at the detention facility, including Omar Khadr, who was classified as a high value detainee by the Obama administration and agreed to a plea agreement after eight years in detention.

The US Department of Defense (DoD) announced April 20 that high-value Guantánamo Bay detainee Abd al-Rahim al-Nashiri will be subject to capital charges and tried in a military court. According to the Pentagon, the chief prosecutor for the DoD's Office of Military Commissions plans to charge al-Nashiri with orchestrating the 2000 attack on the USS Cole that left 17 dead and 40 injured. The office will also bring charges in connection with an attack that same year on a French oil freighter that claimed the life of one crewmember and spilled 90,000 barrels of oil into the Gulf of Aden.

A former Guantánamo Bay detainee announced April 15 that he is suing members of former Egyptian president Hosni Mubarak's regime over allegations that he was tortured by the government while in Egyptian custody. Mamdouh Habib, an Australian citizen, was arrested in Pakistan in 2001 following the 9-11 terrorist attacks on the US. He was released from Guantánamo in 2005 without charges being filed against him, after being held at the detention facility for three years. Habib claims that he was tortured and beaten after being taken to Egypt as part of the CIA's "extraordinary rendition" program. He claims Egypt's former vice-president Omar Suleiman and Mubarak's son Gamal supervised the torture, and indicated that he is seeking compensation and that he hopes those responsible will be imprisoned.

US Attorney General Eric Holder announced April 4 that Khalid Sheikh Mohammed and four other co-conspirators will be tried before a military commission for their roles in the 9-11 terrorist attacks. Holder, who wanted the accused be tried before a federal civilian court, referred the cases to the Department of Defense after Congress imposed a series of restrictions barring the transfer of Guantánamo Bay detainees to the US. Holder said he refused to delay the trial any longer for the sake of the victims of the 9-11 attacks and their families, explaining that the restrictions are not likely to be repealed in the immediate future. While deciding to proceed with military commissions, Holder defended the federal judiciary, saying:

The US Court of Appeals for the District of Columbia Circuit on March 29 overturned a lower court's decision granting release to Yemeni Guantánamo Bay detainee Uthman Abdul Rahim Mohammed Uthman. Uthman's 2004 habeas corpus petition challenging his basis for detention was granted when the US District Court for the District of Columbia determined that the government had failed to prove by a preponderance of the evidence that Uthman had received and executed orders from al-Qaeda. The appeals court rejected this "command structure test" used by the lower court and struck down the ruling, blocking Uthman's release. The appeals court found that decisions made since Uthman's petition dictate that, regarding the detention authority granted by the 2001 Authorization for Use of Military Force (AUMF)], determinations of whether individuals are al-Qaeda members must employ a functional approach on a case-by-case basis, rather than the formal approach used in Uthman's case.

Sen. John McCain (R-AZ), along with five co-sponsors, introduced legislation March 10 that would prohibit funding for civilian trials of Guantánamo Bay detainees and place restrictions on the transfer of detainees to foreign countries. The Military Detainee Procedures Improvement Act of 2011 would require "greater scrutiny on the security situation and ability of the host country to monitor a detainee" after transfer from Guantánamo. It also purports to "[r]eaffirm[] the President's authority to detain members of al-Qaeda, the Taliban, and affiliated terrorist groups based on the authority granted by Congress in the Authorization for Use of Military Force." The legislation would require members of terrorists groups affiliated with al-Qaeda and the Taliban to be held in military custody when captured, and require annual review of whether detainees can be released.

US President Barack Obama on March 7 issued an executive order allowing military commissions for Guantánamo Bay detainees to resume. New charges in the military commission system have been suspended since shortly after Obama took office in 2009. The new order also establishes a procedure for establishing a review process for detainees who have not been charged, convicted or designated for transfer. In a statement, Obama said: