Following the outbreak of the Second World War, Scanlan was called up from the Reserve of Officers (having been placed on the reserve in 1920) and put in command of the 6th Garrison Battalion. In September 1941 he was put in command of Lark Force, which was tasked with the defence of Rabaul, in New Britain. Lark Force was a mixture of regular Australian Army troops (the bulk of whom came from the &lt;a href="2/22nd%20Battalion%20%28Australia%29"&gt;2/22nd Battalion&lt;/a&gt;) and locally raised militia, a total of 1,400 men. When the Japanese Empire invaded Rabaul on 23 January 1942 in what is now known as the Battle of Rabaul, the force was quickly overrun and forced to take to the jungle. When 160 captured Australian soldiers were massacred by the Japanese, Scanlan opted to surrender. He spent the remainder of the war as a prisoner of war.