In November 2008, Department of Defence officials announced that Kohlmann was relinquishing his duties as the Military Judge in the military commissions of the 9-11 hijackers. Due to his impending retirement, Kohlmann detailed Colonel Stephen Henley, U.S. Army, to replace him as the Military Judge in the 9-11 cases. Kohlmann continued to serve as the Chief Judge of the Military Commissions until December 2008. He was succeeded in that position by Colonel James Pohl, U.S. Army. Kohlmann accepted a position as a civilian attorney in the Department of the Navy Office of General Counsel in January 2009.