In his appointed role as chaplain, Yee ministered to Muslim detainees held at Guantánamo Bay detention camp and received commendation from his superiors for his work. When returning from duty at the Guantanamo Bay Naval Base, he was arrested on September 10, 2003, in Jacksonville, Florida, when a U.S. Customs agent found a list of Guantanamo detainees and interrogators among his belongings."Muslim chaplain proposes to resign", by James Polk and Bob Franken, CNN, 5 May 2004 He was charged with five offenses: sedition, aiding the enemy, spying, espionage, and failure to obey a general order. These charges were later reduced to mishandling classified information in addition to some minor charges. He was then transferred to a United States Navy brig in Charleston, South Carolina. The government did not name the country or entity for whom it suspected Yee was spying.
