After a brief involvement with Marxism in 1939, Parsons converted to Thelema, the English occultist Aleister Crowley's new religious movement. In 1941, with his first wife Helen Northrup, Parsons joined the Agape Lodge, the Californian branch of the Thelemite Ordo Templi Orientis (O.T.O.). At Crowley's bidding, he replaced Wilfred Talbot Smith as its leader in 1942 and ran the Lodge from his mansion on Orange Grove Boulevard. Parsons was expelled from JPL and Aerojet in 1944 due to the Lodge's infamous reputation and his hazardous workplace conduct.

In 1945 Parsons separated from Helen after having an affair with her sister Sara; when Sara left him for L. Ron Hubbard, he conducted the Babalon Working, a series of rituals designed to invoke the Thelemic goddess Babalon to Earth. He and Hubbard continued the procedure with Marjorie Cameron, whom Parsons married in 1946. After Hubbard and Sara defrauded him of his life savings, Parsons resigned from the O.T.O. and held various jobs while acting as a consultant for Israel's rocket program. Amid the climate of McCarthyism, he was accused of espionage and left unable to work in rocketry. In 1952 Parsons died at the age of 37 in a home laboratory explosion that attracted national media attention; the police ruled it an accident, but many associates suspected suicide or murder.

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L Ron Hubbard stole his wife and his life savings! And that's not all!