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.[4] 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.[5] 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.[5] 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.