A good deal of the chaplain's career was spent with the U.S. Marines. From time to time he was involved in such controversial issues as compulsory chapel attendance, civil liberties, the rule of law in society, the draft, freedom of the press, and the position of the chaplain in the hierarchy of command. Jones graduated from Andover Newton Theological Seminary in 1940 and joined the Navy in 1942. His duties included: Third Marine Regiment in Samoa, New Zealand, Guadalcanal, Truk, Bougainville; station chaplain at Naval Air Station, Quonset Point, Rhode Island; First Marine Division, FMF Pac in Korea; senior chaplain, Marine Corps Recruit Depot, Parris Island; director, Marine Corps Educational Center at Quantico; staff of Chief, U.S. Naval Forces Europe; and Assistant for Administration, Office of the Chief of Chaplains.