He joined the Royal Canadian Air Force in 1939 as a
flight lieutenant, completed an advanced course and served until mid-1941 as instructor of
British Commonwealth Air Training Plan instructors. After a short period in England at a glider and paratrooper training center, he was posted to No. 405 Squadron RCAF. On returning in difficult weather conditions after bombing Berlin with the squadron on the night of 7 November 1941, he was forced to land his aircraft on a non-operational airfield, and as a result was temporarily suspected of being a spy by the
Home Guard. By February 1942, Fauquier had been promoted to acting
wing commander and given command of the squadron. He was awarded the
Distinguished Flying Cross (DFC) for gallantry. Shortly afterwards he was transferred from operations to the
RCAF's Overseas Headquarters for
staff duties. He then served a short term with
No. 6 Group before once more taking command of No. 405 Squadron in February 1942. During
Operation Hydra in August 1943, a bombing raid on a German military research facility at
Peenemünde, he acted as deputy master bomber, making 17 passes over the target. He was awarded the
Distinguished Service Order (DSO) in September 1943, in part for his leadership during the raid. Soon after that raid he was promoted to acting
group captain of that squadron, which had become a member of
No. 8 (Pathfinder) Group. During January 1944, he flew 38 sorties, completing his second tour of operations with No. 405 Squadron. He was then awarded a
Bar to his DSO. After promotion to acting
air commodore—a rank precluded from operational flying—he was
Mentioned in Dispatches in December 1944. He then voluntarily reverted to group captain so that he might begin a third tour of operations, this time as commanding officer of No. 617 Squadron RAF (the Dambusters squadron), which he led from December until the end of the war. Under his command the Dambusters conducted raids against submarine pens, viaducts and other targets. With the end of the war in Europe, he was awarded a second Bar to his DSO for his command of 617 Squadron. Spencer Dunmore, a historian and novelist, remembers Fauquier in his history of
Canada's Air Force during World War II: ==Post-war==