In Camp Wheeler in Georgia, Father Emil served 19,000 service men and women from October of 1944 to April of 1945, tirelessly providing religious services, making hospital visits, solemnizing marriages, baptizing, and burying. Then he was sent to the India-Burma theater, where he would travel 2,000 miles to have Mass for the troops. He found a deserted Baptist church and readied it for Catholic service. He celebrated several Masses on Sundays in various buildings, such as the army mess hall, a Red Cross facility, or a local theater. Without regard for his personal safety, he worked night and day to serve his troops. In the ceremony making him a captain, he was described as "an untiring conscientious worker".

In April, 1946, Father Emil received orders to return to the States. He received his final pay check of $870.89 and became a civilian once again. He made an intense retreat at Conception and then supplied for the pastor of Strong City who was on vacation. For a short time he was administrator of St. John Church in Spearville, and he served a short time in Hutchinson. Bishop Winkelmann then sent him to Catholic University in Washington, D.C. for an M.A. in education, which he completed in 1948. The bishop queried, "Couldn’t he serve as administrator in accredited diocesan high schools?" Even as a graduate student, Father Emil assisted his fellow priests at Fort Myers in Virginia and at the Shrine of the Immaculate Conception. He didn’t have money to travel home for Christmas in 1947, so he assisted at a Maryland parish.

From April to September of 1948, Father Emil was assigned to Holy Trinity in Timken, Kansas, where he endeared himself as a holy and generous pastor. Fred Tuzicka, who was struggling about a possible priestly vocation said, "He saved my religious vocation." The Korean conflict was then in full bloom, and Father Emil re-enlisted in the Army, serving at Fort Bliss, Texas until December, 1949. Yet another abandoned army chapel had to be cleaned for religious services.

With an abundance of dust storms and ants, the base could hardly be called Fort Bliss, but again he courageously tended to his duties of baptizing, instructing would-be converts, visiting the sick, and ministering to those in need. Father Emil was convinced that being an army chaplain was a call from God. For the last time, he bade farewell to his beloved parents and sailed for Japan in mid-January, 1950.

In the defeated nation of Japan, Father Emil found an army of men immature and not interested in religion. He knew he would have an enormous task to instill some enthusiasm for life in general and in religion in particular. According to the chaplain’s manual, he was "to guide the molding of the mature character of his men over long periods of purposeful training." His studies in Catholic university stood him in good stead as an expert planner and administrator. He celebrated Masses at various locations, officiated at weddings, and provided pre-nuptial instructions. One of his great disappointments was that so few of the troops in Japan received the Eucharist.

He wrote to Bishop Carroll, "I love this kind of work even though the figures are not a true scale of one’s efforts." To another he wrote, "Making 1,100 miles in a jeep on these bumpy mountain roads puts color in a person’s cheeks and calluses on the extremity which has to bear the bumps and bruises." It was not uncommon for Father Emil to travel 800 miles to conduct services for his soldiers.

In July, 1950, Father Emil’s unit landed in South Korea during a big invasion, a clash between Soviet Communism and the United States. From the start, Father Emil had a reputation for courage and concern for the well-being of his men. Casualties began immediately; he ministered to the wounded; he buried the dead; he consoled the grieving families back home by his letters of sympathy. "This fighting is nerve-wracking. Many of my soldiers crack up — they go insane and scream like wild men."

Torrential rains, 100 degree weather, flies, mildew, rusty weapons and sporadic meals of canned foods, little time and place for sleep, constant retreating of the soldiers, refugees ever on the move away from battle lines ... these were a few of the "inconveniences" of life on the battlefield.

Father Emil continued to administer to the dead and dying, burying the almost countless casualties, performing baptisms, hearing first confessions for Holy Communion, celebrating Mass on an improvised altar on the front end of a jeep. Through it all, Father Emil managed to keep up his own morale and that of his men. The GI’s saw him as tireless and fearless, generous beyond words, being the good Samaritan to friend and foe alike. He had a close call when a North Korean’s sniper missed Father Emil’s head by inches but clipped the stem of his treasured pipe.