In 2002, Bush declared that the Geneva Conventions didn’t apply to the stateless, plainclothes "unlawful enemy combatants" of al-Qaida and the Taliban. The Department of Justice then sanctioned interrogation methods such as waterboarding and forced nudity. After Congress and the Supreme Court curbed the administration’s policy, Bush signed an executive order in 2007 allowing the CIA to continue using some harsh tactics.

On his first day in office, Obama revoked Bush’s executive order and limited interrogation tactics to those outlined in the Army Field Manual.

In August, an administration task force recommended creating an interagency group, composed of experienced interrogators and housed within the FBI, that would conduct some interrogations and develop a set of best practices for others.

The Obama administration has taken a clear stance against using evidence obtained through torture or coercion. Attorney General Eric Holder has also appointed a special prosecutor to investigate whether CIA interrogators overseas broke the law, although he has said he will not prosecute anyone who followed the Bush administration’s interrogation guidelines.

Beginning in 2002, the Bush administration expanded what’s known as extraordinary rendition. Through the program, CIA agents abducted and transported terrorism suspects to countries such as Egypt and Afghanistan for interrogation. During the same period, the CIA also operated its own secret prisons, or "black sites," abroad.

On his first day in office, Obama issued an executive order to close the CIA prisons. But the agency still has permission to detain prisoners on a "short-term, transitory basis." In its August statement, Obama’s interrogation task force announced that renditions could continue, but that the government would monitor rendered individuals more closely to ensure they were not tortured. The recommended safeguards include "diplomatic assurances"; an annual evaluation by inspectors general from the Pentagon, the State Department and the Department of Homeland Security; and a "monitoring mechanism" that provides private access to prisoners with little advance notice.Human rights activists have expressed doubts that diplomatic assurances from countries receiving prisoners are any more trustworthy than they were during the Bush administration.

The Obama administration has also limited attempts at accountability for past renditions: In a lawsuit filed against a Boeing subsidiary involved in rendition transport, the administration has upheld the Bush precedent of classifying the program as a "state secret." This has essentially halted attempts to seek restitution by some who say they were imprisoned because of mistaken identity.

Bush suspended habeas corpus rights for prisoners deemed unlawful enemy combatants. In 2008, the Supreme Court ruled that prisoners in Guantanamo had the right to challenge their detentions in U.S. federal court.

Obama issued an executive order on his first day in office mandating the closure of Guantanamo by Jan. 22, 2010, but the administration has faced obstacles in making that happen.

In ongoing lawsuits, the Obama administration has upheld the government’s right to hold Guantanamo prisoners indefinitely, and as ProPublica has reported, the government continues to hold some who have been cleared for release in federal courts.

Beyond Guantanamo, the current administration has maintained the Bush administration’s position of preventive detention, contending that habeas rights do not extend to prisoners held at facilities such as Bagram, even those detained outside Afghanistan. (See ProPublica’s previous reporting on that issue, as well as the Obama administration’s latest explanation of its position.) Human rights activists point out that Bagram now holds three times as many prisoners as Guantanamo, although the exact number and who they are remain undisclosed.

In June, ProPublica reported that Obama was drafting an executive order to allow indefinite detention. While the president later expressed pause about giving such an order, he has said that "there may be a number of people who cannot be prosecuted for past crimes," an indication that some prisoners may be held indefinitely.

In a 2001 executive order, Bush wrote that prisoners eligible for trial would be tried in military commissions rather than in U.S. courts, which allowed for greater application of secrecy and looser rules about admissible evidence. In 2006, the Supreme Court declared the commissions unlawful. Congress responded by passing the Military Commissions Act of 2006 to legalize their continued use.

After initially suspending military commissions, Obama’s detention task force issued a preliminary report stating they would continue to be used when evidence in a case did not meet the standards of criminal court. The administration promised five changes to commission rules that it contends legitimize commissions as a form of trial, including prohibition of evidence obtained through torture and ensuring that the alleged offenses are "war offenses." For prisoners in Guantanamo, Obama’s detention task force stated that a legal team will determine the appropriate forum for prosecution, as well as "whether the case is feasible for prosecution."

The changes have not satisfied human rights advocates, who contend that the military commissions still represent a substandard form of justice. Advocates also point to a strong record of successful prosecution of terrorism suspects in federal court.

Bush angered transparency advocates by initiating a policy that discouraged granting Freedom of Information Act requests. He also expanded the classification of documents and invoked the "state secrets" rule in court.

Obama reversed the Bush-era FOIA rules, and declassified some previously secret legal memos, most notably those authorizing abusive interrogations. The administration has continued to keep some documents secret, however, including photos of prisoner abuse. As the Washington Independent has documented, the administration is likely withholding documents related to CIA interrogations sought by the ACLU in spite of a court order to release them. The administration has also continued to invoke the "state secrets" rule in court.

After Sept. 11, 2001, Bush authorized the creation of a program allowing intelligence agencies to intercept some phone calls into and out of the United States without a warrant. Bush acknowledged the previously secret program after it was disclosed by The New York Times in 2005. In 2008, Congress legalized the effort, expanding the National Security Agency’s ability to investigate individuals believed to be overseas. The ACLU has argued that the amendment is unconstitutional.

As a senator, Obama supported the 2008 legislative amendments. In lawsuits related to the surveillance program, the Obama administration has upheld the Bush administration’s "state secrets" stance, making it difficult to learn the true extent of the program. Human rights advocates say that thus far there is no evidence that the Obama administration has targeted Americans for surveillance without court permission. But they also say the administration’s position on some of the broad surveillance measures the new law allows is still unclear.