It prohibited detainees who had been classified as enemy combatants or were awaiting hearings on their status from using habeas corpus to petition federal courts in challenges to their detention.

In Boumediene v. Bush (2008), the Supreme Court held that Section 7 of the law was unconstitutional because of its restrictions of detainee rights under the Suspension Clause.

It is defined in the US Army Field Manual, section 27–10, for the purpose of determining whether a person is or is not entitled to prisoner of war status, and consists of a board of not less than three officers.

The American Civil Liberties Union summarized the positive aspects as "restricting coerced and hearsay evidence and providing greater defense counsel resources."

[8] While formally opposed to the Act, Human Rights Watch has also concluded that the new law limits the scope of trials by military commissions to non-US citizens including all legal aliens.

Supporters of the act say that the Constitutional provision guaranteeing habeas corpus does not apply to alien enemy combatants engaged in hostilities against the United States, and that the provisions of the Act removing habeas corpus do not apply to United States citizens; they conclude that therefore the law does not conflict with the Constitution.

National Review columnist Andrew McCarthy argued that since the law applies to "aliens with no immigration status who are captured and held outside the territorial jurisdiction of the United States, and whose only connection to our country is to wage a barbaric war against it" they do not have a constitutional right to habeas corpus.

"[15] John Yoo, a former Bush Administration Justice Department official and current professor of law at the University of California, Berkeley, called the Act a "stinging rebuke" of the Supreme Court's Hamdan v. Rumsfeld ruling, calling that ruling "an unprecedented attempt by the court to rewrite the law of war and intrude into war policy."

[16] Formerly Lieutenant Colonel in the US Army Judge Advocate General's Corps and current professor at St. Mary's University School of Law, Jeffrey Addicott wrote "the new Military Commissions Act reflects a clear and much-needed Congressional commitment to the war on terror, which to this point has been largely conducted in legal terms by the executive branch with occasional interjections from the judiciary".

[21] In the House debate, Representative David Wu of Oregon offered this scenario: Let us say that my wife, who is here in the gallery with us tonight, a sixth generation Oregonian, is walking by the friendly, local military base and is picked up as an unlawful enemy combatant.

[22]Following debate in the House and Senate, the final law revoked Habeas Corpus protections only for non-citizens: (e)(1) No court, justice, or judge shall have jurisdiction to hear or consider an application for a writ of habeas corpus filed by or on behalf of an alien detained by the United States who has been determined by the United States to have been properly detained as an enemy combatant or is awaiting such determination.Hence in the preceding example, if Wu's wife, a citizen, were picked up outside a military base, Wu could walk across the street and file a habeas corpus petition with the courts.

[23][29] Passing laws that remove the few checks against mistreatment of prisoners will not help us win the battle for the hearts and minds of the generation of young people around the world being recruited by Osama bin Laden and al Qaeda.

Authorizing indefinite detention of anybody the Government designates, without any proceeding and without any recourse—is what our worst critics claim the United States would do, not what American values, traditions and our rule of law would have us do.

[30]One Bush administration critic described the Act as "the legalization of the José Padilla treatment"—referring to the American citizen who was declared an unlawful enemy combatant and then imprisoned for three years before finally being charged with a lesser crime than was originally alleged.

"[33] Joanne Mariner, an attorney who serves as the Terrorism and Counterterrorism Program Director at Human Rights Watch, described the issue this way: The MCA states that it does not create any new crimes, but simply codifies offenses "that have traditionally been triable by military commissions."

In Hamdan v. Rumsfeld, however, a plurality of the Supreme Court (four justices) found that conspiracy—one of the offenses enumerated in the MCA—was not a crime triable by military commission.

The specific actions defined in section 6 of the Military Commissions Act include torture, cruel or inhumane treatment, murder, mutilation or maiming, intentionally causing serious bodily harm, rape, sexual assault or abuse, and the taking of hostages.

According to Mariner of Human Rights Watch, the effect is "that perpetrators of several categories of what were war crimes at the time they were committed, can no longer be punished under U.S.

"[36] The Center for Constitutional Rights adds: The MCA's restricted definitions arguably would exempt certain U.S. officials who have implemented or had command responsibility for coercive interrogation techniques from war crimes prosecutions.. ...

Although the provision recognizes the possibility of civil and or criminal proceedings, the Center for Constitutional Rights has criticised this claiming that "The MCA retroactively immunizes some U.S. officials who have engaged in illegal actions which have been authorized by the Executive.

"[39] and an editorial in The New York Times described the Act as "a tyrannical law that will be ranked with the low points in American democracy, our generation's version of the Alien and Sedition Acts,"[4] while American Civil Liberties Union Executive Director Anthony D. Romero said, "The president can now, with the approval of Congress, indefinitely hold people without charge, take away protections against horrific abuse, put people on trial based on hearsay evidence, authorize trials that can sentence people to death based on testimony literally beaten out of witnesses, and slam shut the courthouse door for habeas petitions.

"[40] Jonathan Turley, professor of constitutional law at George Washington University, called the Military Commissions Act of 2006 "a huge sea change for our democracy.

"[41] Nat Hentoff opined in the Village Voice that "conditions of confinement and a total lack of the due process that the Supreme Court ordered in Rasul v. Bush and Hamdan v. Rumsfeld" make US government officials culpable for war crimes.

The outcome of his trial was prescribed by a pre-trial agreement negotiated between Hicks's defense counsel and the convening authority, Susan J. Crawford on March 26, 2007.

[48]In April 2007, the Supreme Court declined to hear two cases challenging the MCA: Boumediene v. Bush and Al Odah v. United States.

The decision, extending habeas corpus rights to alien unlawful enemy combatants but allowing the commissions to continue to prosecute war crimes, was handed down on June 12, 2008.

[50][51] Even though detainees now have the right to challenge the government's basis of their detention, that does not guarantee release as evidenced by the December 14, 2009 ruling of U.S. District Judge Thomas F. Hogan who upheld continued detention of Musa'ab Al-Madhwani in Guantanamo Bay, Cuba even though the court determined that he was not a continuing threat, the government met its burden of proving he was a member of al-Qaeda.