Following the outbreak of World War II, Brain was given the task of coordinating Qantas' support for the Australian military, which became known as the Qantas Merchant Air Service [REF].
By February 1942, Brain was running the Qantas base at Broome in north Western Australia, which had assumed major importance as a way station for evacuees from the Dutch East Indies, possessing a harbour suitable for flying boats, as well as an airfield that could take heavy bombers.