During 2005-2006 Morris served as the Staff Judge Advocate to the Superintendent of the United States Military Academy at West Point. In early 2007 Morris was the Chief of the U.S. Army Trial Defense Service, where he was responsible for the work and professional training of all uniformed Army defense attorneys as they represented soldiers accused of crimes under the
UCMJ. In 2002, Morris was the head of the Army's criminal law branch and was tasked with planning the first prosecution of suspected 9/11 terrorists. According to the Wall Street Journal, back in 2002 "he proposed a high-profile public trial that would lay bare the scope of al Qaeda's alleged conspiracy while burnishing the ideals of American justice." His legal advice was disregarded by the Bush administration, which decided to interrogate terrorists in secret—perhaps to gain critical intelligence necessary—to prevent further attacks, rather than seek justice through high-profile trials. Morris was later asked to conduct the trials.
Comments on the testimony of the witness known as "OC-1" The
Toronto Star identified Morris as the Chief Prosecutor of the
Guantanamo military commissions. The Bush administration acknowledged subjecting Al Qahtani to 58 days of sleep deprivation and other
extreme interrogation methods in the fall of 2002, when intelligence officials realized he had tried to travel to the United States in the months preceding al Qaeda's
September 11 attacks. Morris's prosecution team had proposed charges against Al Qahtani to
Susan Crawford in early 2008. Crawford, the
convening authority of military commissions, has the final say over whether charges are confirmed. She dropped the charges against al Qahtani because his "treatment met the legal definition of torture". During his only testimony that has been made public—his testimony before his 2006
Administrative Review Board hearing—Al Qahtani acknowledged confessing to extensive ties to al Qaeda, and the 9-11 hijacking plot, but he claimed all his confessions were from the two months he was being tortured, and he had recanted them at every opportunity since then. When announcing the new charges, Morris stated that the new charges were based on "independent and reliable evidence". He stated: "His conduct is significant enough that he falls into the category of people who ought to be held accountable by being brought to trial." ==Retirement announcement==