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War on Terror
In the aftermath of the September 11, 2001 attacks, the U.S. Government adopted several new measures in the classification and treatment of prisoners captured in the War on Terror, including applying the status of unlawful combatant to some prisoners, conducting extraordinary renditions, and using torture ("enhanced interrogation techniques"). Human Rights Watch and others described the measures as being illegal under the Geneva Conventions.

Command responsibility
A presidential memorandum of February 7, 2002, authorized U.S. interrogators of prisoners captured during the War in Afghanistan to deny the prisoners basic protections required by the Geneva Conventions, and thus according to Jordan J. Paust, professor of law and formerly a member of the faculty of the Judge Advocate General's School, "necessarily authorized and ordered violations of the Geneva Conventions, which are war crimes." Based on the president's memorandum, U.S. personnel carried out cruel and inhumane treatment on captured enemy fighters, which necessarily means that the president's memorandum was a plan to violate the Geneva Convention, and such a plan constitutes a war crime under the Geneva Conventions, according to Professor Paust.

U.S. Attorney General Alberto Gonzales and others have argued that detainees should be considered "unlawful combatants" and as such not be protected by the Geneva Conventions in multiple memoranda regarding these perceived legal gray areas.

Gonzales' statement that denying coverage under the Geneva Conventions "substantially reduces the threat of domestic criminal prosecution under the War Crimes Act" suggests, to some authors, an awareness by those involved in crafting policies in this area that U.S. officials are involved in acts that could be seen to be war crimes. The U.S. Supreme Court challenged the premise on which this argument is based in Hamdan v. Rumsfeld, in which it ruled that Common Article Three of the Geneva Conventions applies to detainees in Guantanamo Bay and that the military tribunals used to try these suspects were in violation of U.S. and international law.

Human Rights Watch claimed in 2005 that the principle of "command responsibility" could make high-ranking officials within the Bush administration guilty of the numerous war crimes committed during the War on Terror, either with their knowledge or by persons under their control. On April 14, 2006, Human Rights Watch said that Secretary Donald Rumsfeld could be criminally liable for his alleged involvement in the abuse of Mohammed al-Qahtani. On November 14, 2006, invoking universal jurisdiction, legal proceedings were started in Germany – for their alleged involvement of prisoner abuse – against Donald Rumsfeld, Alberto Gonzales, John Yoo, George Tenet and others.

The Military Commissions Act of 2006 is seen by some as an amnesty law for crimes committed in the War on Terror by retroactively rewriting the War Crimes Act and by abolishing habeas corpus, effectively making it impossible for detainees to challenge crimes committed against them.

Luis Moreno-Ocampo told The Sunday Telegraph in 2007 that he was willing to start an inquiry by the International Criminal Court (ICC), and possibly a trial, for war crimes committed in Iraq involving British Prime Minister Tony Blair and American President George W. Bush. Though under the Rome Statute, the ICC has no jurisdiction over Bush, since the U.S. is not a State Party to the relevant treaty—unless Bush were accused of crimes inside a State Party, or the UN Security Council (where the U.S. has a veto) requested an investigation. However, Blair does fall under ICC jurisdiction as Britain is a State Party.

Shortly before the end of President Bush's second term in 2009, newsmedia in countries other than the U.S. began publishing the views of those who believe that under the United Nations Convention Against Torture, the U.S. is obligated to hold those responsible for prisoner abuse to account under criminal law. One proponent of this view was the United Nations Special Rapporteur on torture and other cruel, inhuman or degrading treatment or punishment (Professor Manfred Nowak) who, on January 20, 2009, remarked on German television that former president George W. Bush had lost his head of state immunity and under international law the U.S. would now be mandated to start criminal proceedings against all those involved in these violations of the UN Convention Against Torture. Law professor Dietmar Herz explained Nowak's comments by opining that under U.S. and international law former President Bush is criminally responsible for adopting torture as an interrogation tool.

Haditha Killings

On November 19, 2005 in Haditha, Iraq, Staff Sgt. Frank Wuterich led Marines from the 3rd battalion into Haditha. In Al-Subhani, a neighborhood in Haditha, Lance Cpl. Miguel Terrazas (20 years old) was killed by a roadside bomb. Later in the day, 24 Iraqi women and children were found dead and suspicion fell on Staff Sgt. Frank Wuterich and his marines. Wuterich acknowledged in military court that he gave his men the order to "shoot first, ask questions later" after the roadside bomb explosion. Wuterich told military judge Lt. Col. David Jones "I never fired my weapon at any women or children that day." On January 24, 2012, Frank Wuterich was given a sentence of just 90 days in prison along with a reduction in rank and pay. Just a day before, Wuterich pled guilty to one count of negligent dereliction of duty. No other marine that was involved that day got any jail time.

Azizabad airstrike

On August 28, 2008 around midnight, a U.S. airstrike killed 90 people including 60 children in an Afghan village. After conducting a report in the Afghan village, the UN had found evidence that confirmed that 90 people including 60 children were killed in the airstrike. The report also found that at least 15 people had been wounded by the airstrike. Even after the UN reports, the U.S. maintained that the number of causalities was much lower than what the UN and Afghan officials claim. The head of the parliamentary defense committee and a member of the government commission, Mohammad Iqbal Safi, has maintained that 90 people were killed including 60 children ranging from 3 months to 16 years old.