During the Gulf War, Auger led the first two Canadian Forces Advanced Surgical Teams into Saudi Arabia (Operation Scalpel) as part of the Canadian Government's commitment to the Gulf War (Operation Desert Storm) in 1991. In the summer of the same year, Auger was transferred to Ottawa, as Chief of Surgery at the National Defence Medical Centre (NDMC), a position he held until 1996. During this posting he was deployed to Somalia and twice to Bosnia as a surgeon with the Advanced Surgical Centre.