He enlisted in the USAAF in Milwaukee, Wisconsin, on 28 January 1942. He completed fighter pilot training and earned his commission and pilot wings. On 9 July 1944, a flight of P-51-A-10 Mustangs, including # 43-6282, assigned to the 311th Fighter Group, 530th Fighter Squadron, took off from the 10th Air Force field at Tingkawk Sakan, India, on a mission to intercept enemy aircraft south of Myitkyina, Burma. A P-51-A-10, 43-6282, flown by Capt. John F. Emery, 0-665185, was shot down by enemy fighters 20 miles south of Sahmaw, Burma, at about 1305 hours. Immediately after enemy fighters dove on B-25s and then fired on their formation, 2ndLt. Wall saw Emery break away on a 30-degree dive with coolant streaming from under the fuselage. 1stLt Wilbourne saw a P-51 below him make passes at an enemy Oscar. He joined in that chase south down the Irrawady to the bottom of the Love-William area. He shot off the tail of an Oscar then pulled up sharply. He lost sight of the other P-51 and the other Oscar underneath. He was jumped by a Zero and took evasive action into clouds. About 15 minutes later, over Bhamo, he heard whom he thought was Emery calling on GI 3, and gave his position as 20 miles south of Sahmaw. He reported 3 Tojos at that position. He heard no other radio reports. Capt. Emery is remembered on the memoral wall at the Manila American Cemetery & Memorial, Philippines. He was awarded the Distinguished Flying Cross, Air Medal and Purple Heart.
His brother, Valmer C. Emery Jr., served in the USAAF as a pilot of a B-26 bomber. During training on a flight from Dodge Field, Dodge City, Kansas, and near Wold-Chamberlain Field, Minnesota, the pilots of the B-26 “dived [the bomber] in an heroic attempt to avoid hitting residences.” Killed were: Lt. T.J. Reach, 22, Chicago; Lt. Valmer C. Emery Jr., 24, Milwaukee; Lt. Arnold M. Bridges, 22, Detroit; Sgt. Leo G. Wantuck, 24, Michigan City, Indiana; Sgt. A.D. Bronk, 25, Ravens, N.Y.; and Pvt. Frank C. Spiecker, 21, Lockport, IL. Witnesses said the bomber swopped sharply off its course, banked, then plunged nose down into the ground. A moment later, it became a flaming death pyre as a terrific explosion was followed closely by a second. The bomber grazed trees, telephone wires and garages, and narrowly missed Morris Park school where several hundred children attended classes. The wreckage was in vacant lots where a short time before several youngsters were playing.