He returned to the Ministry of Defence as Director of Air Force Plans and Programmes in 1987 and then became Assistant Chief of Defence Staff, Operational Requirements (Air) in 1989. Allison was appointed Air Officer Commanding No. 11 Group in 1991. He went to become Chief of Staff and Deputy Commander-in-Chief of RAF Strike Command in 1994 and then Commander-in-Chief of RAF Logistics Command in 1996. He served as Air Officer Commanding RAF Strike Command from 25 July 1997 to 28 March 1999 when he retired from the Royal Air Force.