Sweeney became an instructor in the atomic missions training project, Project Alberta, at Wendover Army Airfield, Utah. Selected to be part of the 509th Composite Group commanded by Col. Paul Tibbets, he was named commander of the 320th Troop Carrier Squadron on 6 January 1945. Initially his squadron used C-47 Skytrain and C-46 Commando transports on hand to conduct the top secret operations to supply the 509th, but in April 1945 it acquired five C-54 Skymasters, which had the range to deliver personnel and materiel to the western Pacific area.