After he was released from active duty Wherley served in a number of staff assignments with the National Guard in Maryland, and for a short time deployed as the deputy operations group commander for fighters at Prince Sultan Air Base in Saudi Arabia. As a pilot and instructor, he clocked up more than 5,000 hours of flying time over a multitude of missions.[1]
Wherley gained his first command in 1985 with the 121st Fighter Squadron, and went on to command Detachment 1 (later to be re-designated 201st Airlift Squadron).[1]
At the time of the 9/11 attacks in 2001, Wherley was commander of 113th Wing, the Guard unit responsible for protecting Washington D.C. That morning, Wherley ordered his pilots, who did not launch until after the Pentagon attack, to operate weapons free, meaning that they were permitted to shoot at will.[3]
Wherley was appointed commanding general of the District of Columbia National Guard in 2003. He retired from that position and from the Air Force in 2008.[1]
March 1989 – November 1995, commander, Detachment 1/201st Airlift Squadron, Headquarters, District of Columbia Air National Guard, later Andrews Air Force Base, Maryland.
November 1995 – December 1997, vice commander, 113th Wing, Andrews Air Force Base, Maryland.
^The date of death on the Wherley's headstones is June 23 – the day after the train crash. Some bodies were not discovered in the train wreckage until June 23