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In 2011, Shaye was arrested, beaten, and held in solitary confinement for 34 days in Yemen. He was eventually tried and convicted of terrorism-related charges and sentenced to five years in prison, followed by two years of restricted movement and government surveillance. His conviction and sentencing was deeply unpopular with the Yemeni populace.
On February 2, 2011, President Obama called then-Yemeni President Ali Abdullah Saleh to discuss counterterrorism cooperation and Al Qaeda in the Arabian Peninsula. At the end of the call, according to a White House read-out, Obama “expressed concern” over the release of Shaye. Shaye had not been released at the time of the call, but Saleh did have a pardon prepared.
Consequently Shaye was not released until 2013. Shaye reported that the site of the al-Majalah bombing was littered with remnants of U.S. Tomahawk missiles and cluster munitions, contradicting claims by the government of Yemen that the bombing was their own. U.S. responsibility was denied by Pentagon officials but later confirmed by Amnesty International, The Telegraph newspaper, and a release of secret materials by Wikileaks.
He also reported that 21 children and 14 women had been killed in the bombing. On August 16, 2010, Shaye was arrested by the Yemeni government. After 34 days of confinement, he was convicted of "terrorism-related charges" in a trial regarded by Amnesty International, Human Rights Watch, Committee to Protect Journalists, and the International Federation of Journalists as a sham trial and sentenced to 5 years imprisonment.
After a public outcry from tribal leaders in Yemen over Shaye's imprisonment, Yemeni president Ali Abdullah Saleh was prepared to release Shaye, but he was swayed otherwise by a call from U.S. President Barack Obama on February 2, 2011 citing his "concern" over Shaye's imminent release. Journalist Jeremy Scahill reported that, according to his sources in Yemen, Saleh rescinded his pardon primarily due to the call from President Obama. Scahill suggested that Yemen's counter-terrorism funding from the United States may have motivated Saleh's cooperation.
On July 23, 2013, Shaye was released from prison to serve out the remaining 2 years of his 5-year sentence under house arrest. Dirty Wars, a 2013 American documentary directed by Richard Rowley, and written by Jeremy Scahill and David Riker.