In February 1942, two months after the Japanese attack on Pearl Harbor, his entire R.O.T.C. (Reserve Officers Training Corps) class was called to active duty, and he served as an officer in Ordnance. He took part in the Normandy invasion, the liberation of France and Belgium, and the occupation of Germany. He was recalled to active duty to serve in the Korean War, eventually reaching the rank of Major. He was recalled again for another tour of duty in Korea in the early 1960s, then six months prior to completing 30 years Reserve service, he was mustered out during a RIF (Reduction In Force), thus losing what would have been an earned pension. His "retired" rank was Lieutenant Colonel. He continued his studies as a civilian between tours of duty, with both a bachelor's degree and a master's degree in Political Science from the University of California, Berkeley.
During World War II, especially when he was stationed in England in 1943 and the first half of 1944, McMurtry was able to meet with and become a personal student of Aleister Crowley, who elevated him to IX° of O.T.O., giving him the name Hymenaeus Alpha (which enumerates to 777) in November 1943. In September and November 1944 (and once again in June 1947) he received letters from Crowley referring to him as Crowley's "Caliph" (or eventual successor). When McMurtry returned to California after the war he was appointed Crowley's O.T.O. representative in the United States (April 1946) subject only to the authority of Crowley's viceroy and heir apparent, Karl Germer.
Crowley died in December 1947, and Germer was recognized as the head of O.T.O. At the time the only functioning Thelemic O.T.O. body in the world was Agape Lodge in Southern California, which was headed for a time by McMurtry's friend Jack Parsons. McMurtry planned to start a lodge in Northern California, but his deteriorating relationship with Karl Germer (based on Germer's refusal to initiate new members) put an end to his plans. He tried to organize other O.T.O. members in California to lobby Germer to change his policy, but the situation came to a head at a meeting in 1959 in which Dr. Gabriel Montenegro (Germer's representative) "ordered" McMurtry to cease his efforts. This order was reiterated in writing in November 1960. He unwillingly complied with the order, and McMurtry was disillusioned enough by this turn of events to end his direct involvement with O.T.O. In 1961 he moved to Washington, D.C., where he soon became completely out of touch with other O.T.O. members.
There were a few individuals, notably Kenneth Grant of Britain, Hermann Metzger of Switzerland, and later, Marcelo Ramos Motta of Brazil, who claimed succession to Germer. McMurtry was unaware of any of these developments until 1968, when he received a letter from Phyllis Seckler, a fellow Agape Lodge O.T.O. initiate.
Seckler's letter was to inform McMurtry that the archives in Germer's widow's care (including Aleister Crowley's library) had been burglarized the previous year by persons unknown. When he became aware of the situation he decided to take charge of what remained of the O.T.O. In 1969 he left his job at the United States Department of Labor and returned to California to investigate the burglary. Though the crime was never officially solved, McMurtry felt that it had probably been carried out by a group, falsely claiming affiliation with O.T.O., that called itself "Solar Lodge". He had moved into Seckler's home in Dublin, California, and soon they were married.
At this time, McMurtry decided to restore the Order by invoking his emergency orders from Crowley which gave him authority (subject to Karl Germer's approval) to "take charge of the whole work of the Order in California to reform the Organization", and he assumed the title "Caliph of O.T.O.," as specified in Crowley's letters to McMurtry from the 1940s. His witnesses were Dr. Israel Regardie (1907-1985) and Gerald Yorke, who both offered their support. Along with Seckler and two other surviving members, Mildred Burlingame and Helen Parsons Smith, he slowly began performing O.T.O. initiations again. They also eventually succeeded in their efforts to find a publisher for the Tarot deck designed by Aleister Crowley. O.T.O. was registered with the State of California on December 28, 1971 as a legal organization. It is curious that previously Seckler had written to Marcelo Motta that he was named as Germer's successor according to his widow. This occurred shortly after Germer's death.
In 1974 McMurtry and Seckler separated, and he moved to Berkeley, California. Germer's widow died in 1975, and in 1976 the surviving members of O.T.O. were enabled by court order to claim the still considerable archives. In October 1977 McMurtry founded Thelema Lodge in Berkeley to serve as the headquarters of his resuscitated O.T.O. Many initiations were performed, and a weekly celebration of the Gnostic Mass was soon established in the San Francisco Bay area. McMurtry, and other initiators chartered by him, established O.T.O. groups in many other areas in the United States and internationally. By 1985 the O.T.O., by its own report, had more than seven hundred members in several different countries. In that year McMurtry, in failing health, successfully sued Motta in United States district court over the possession of the O.T.O. trademarks and copyrights. He died in a San Francisco Bay Area convalescent hospital on the day that the U.S. court clerk released the text of the decision that set the seal on McMurtry's efforts to reestablish the O.T.O. Since then McMurtry's "Caliphate" O.T.O. has, by its own report, grown to over three thousand members in more than fifty countries.