He headed the operations sections until the beginning of March 1942, when he was attached to the Munitions Assignment Board for a brief period. Malony was promoted to the rank of Major General in July 1942 and appointed commanding general of the newly activated 94th Infantry Division at Fort Custer, Michigan. He directed division's training until the beginning of August 1944, when he sailed for Europe. Following a brief stay in England, the 94th landed on Utah Beach, France on D-Day + 94, 8 September 1944, and moved into Brittany to relieve the 6th Armored Division and assume responsibility for containing some 60,000 German troops besieged in their garrisons at the Channel ports of Lorient and Saint-Nazaire. The 94th inflicted over 2,700 casualties on the enemy and took 566 prisoners before being relieved by the 66th Infantry Division on New Year's Day 1945. Malony subsequently led the 94th Division during the combats in the Ardennes in Belgium in early 1945. His participated in the combats on the Siegfried Line and secured the area from Orscholz and Saarburg to the confluence of the Saar and Moselle Rivers by 21 February 1945. Malony and 94th Division reached the Rhine on 21 March, where it fought in the Battle for Ludwigshafen. Ludwigshafen was taken on 24 March, in conjunction with Combat Command A of the 12th Armored Division. By 3 April, Malony commanded his division during the assuming responsibility for containing the western side of the Ruhr Pocket from positions along the Rhine. With the reduction of the pocket in mid-April, the division was assigned military government duties, first in the Krefeld and later in the Düsseldorf areas. From mid-June, the division served the military government in Czechoslovakia and Malony was transferred to the United Kingdom at the end of June 1945 for duty with Munitions Assignment Board. For his service with 94th Infantry Division during European campaign, Malony was decorated with his second Army Distinguished Service Medal, Silver Star and Bronze Star Medal. He also received Legion of Honor, rank Officer and "Croix de guerre 1939-1945" with Palm by the Government of France and Belgian "Croix de guerre 1940-1945" with Palm. In November 1945, Malony was assigned as a Representative on International Group to observe Greek elections and stayed in this capacity until May of the next year. He was subsequently appointed a Director of the Historical Division within Department of the Army and served in this capacity until March 31, 1949, when he finally retired from the Army.