In 1999, Colonel Kelly transferred to joint duty and served as the Special Assistant to the Supreme Allied Commander, Europe, in Mons, Belgium. He returned to the United States in 2001, and was assigned to a third tour of duty at Camp Lejeune, now as the Assistant Chief of Staff G-3 with the 2nd Marine Division. In 2002, selected to the rank of Brigadier General, Colonel Kelly again served with the 1st Marine Division, this time as the Assistant Division Commander. Much of Brigadier General Kelly‘s two-year assignment was spent deployed in Iraq. He then returned to Headquarters Marine Corps as the Legislative Assistant to the Commandant from 2004 to 2007. Promoted to major general, he returned to Camp Pendleton as the Commanding General, I Marine Expeditionary Force (Forward). The command deployed to Iraq in early 2008 for a year-long mission, replacing II Marine Expeditionary Force (Forward) as Multinational Force-West in Al Anbar and western Ninewa provinces. LtGen Kelly commanded Marine Forces Reserve and Marine Forces North from October 2009 to March 2011. General Kelly comes to United States Southern Command from his previous position as the Senior Military Assistant to the Secretary of Defense from March 2011 to October 2012.