Following this Honner undertook a training role, serving as commanding officer of an Australian training battalion in the Middle East, to which he was posted in October 1941. Honner returned to Australia in May 1942. After being briefly reunited with his wife he was promoted to lieutenant colonel and sent to Papua where he was given command of the 39th Battalion, who were involved in a desperate campaign against the Japanese forces fighting along the Kokoda Track. With instructions to stop the Japanese advance at Isurava, Honner arrived on 16 August 1942. Upon reaching the battalion's position, Honner found that his new command was already depleted from tropical diseases and from earlier fighting and was heavily outnumbered.