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==== Military career ====
In 1941, Hubbard applied to join the United States Navy. His application was accepted, and he was commissioned as a lieutenant junior grade in the United States Naval Reserve on July 19, 1941. By November, he was posted to New York for training as an intelligence officer. The day after Pearl Harbor, Hubbard was posted to the Philippines and departed the US bound for Australia. But while in Australia awaiting transport to the Philippines, Hubbard was suddenly ordered back to the United States after being accused by the US Naval Attaché to Australia of sending blockade-runner Don Isidro "three thousand miles out of her way".
In June 1942, Hubbard was given command of a patrol boat at the Boston Navy Yard, but he was relieved after the yard commandant wrote that Hubbard was "not temperamentally fitted for independent command". In 1943, Hubbard was given command of a submarine chaser, but only five hours into the shakedown cruise, Hubbard believed he had detected an enemy submarine. Hubbard and crew spent the next 68 hours engaged in combat. An investigation concluded that Hubbard had likely mistaken a "known magnetic deposit" for an enemy sub. The following month, Hubbard unwittingly fired upon Mexican territory and was relieved of command. In 1944, Hubbard served aboard the USS Algol before being transferred. The night before his departure, Hubbard reported the discovery of an attempted sabotage.
In June 1942, Navy records indicate that Hubbard suffered "active conjunctivitis" and later "urethral discharges". After being relieved of command of the sub-chaser, Hubbard began reporting sick, citing a variety of ailments, including ulcers, malaria, and back pains. In July 1943, Hubbard was admitted to the San Diego naval hospital for observation—he would remain there for months. Years later, Hubbard would privately write to himself: "Your stomach trouble you used as an excuse to keep the Navy from punishing you." On April 9, 1945, Hubbard again reported sick and was re-admitted to Oak Knoll Naval Hospital, Oakland. He was discharged from the hospital on December 4, 1945.
==== After the war ====
After Hubbard chose to stay in California rather than return to his family in Washington state, he moved into the Pasadena mansion of John "Jack" Whiteside Parsons, a rocket propulsion engineer and a leading follower of the English occultist Aleister Crowley. Hubbard befriended Parsons and soon became sexually involved with Parsons's 21-year-old girlfriend, Sara "Betty" Northrup. Hubbard and Parsons collaborated on "Babalon Working", a series of sex magic rituals intended to summon an incarnation of Babalon, the supreme Goddess in Crowley's pantheon. According to religious studies scholar Hugh Urban, Parsons' own account of the period, The Book of Babalon, describes the workings as occult ceremonies based on Crowley's teaching, requiring a woman to take part in sexual rites meant to bring about the birth of a spiritual being sometimes described in Thelemic literature as a "moonchild" – a supernatural offspring "mightier than all the kings of the Earth". Parsons viewed Hubbard as being unusually sensitive to occult forces and brought him into the project as an active collaborator. He assigned Hubbard the role of "Scribe", responsible for channelling messages attributed to Babalon. One ritual account from March 1946 describes Hubbard speaking in the goddess's voice, portraying her as the "flame of life, power of darkness" who "feeds upon the death of men". In 1969, the Church of Scientology acknowledged that these rites had occurred and claimed that Hubbard's involvement had been an effort to rescue Betty.
During this period, Hubbard authored a document which has been called the "Affirmations", a series of statements relating to various physical, sexual, psychological and social issues that he was encountering in his life. The Affirmations appear to have been intended to be used as a form of self-hypnosis with the intention of resolving the author's psychological problems and instilling a positive mental attitude.
Parsons, Hubbard and Sara invested nearly their entire savings — the vast majority contributed by Parsons and Sara — in a plan for Hubbard and Sara to buy yachts on the East Coast and sail them to the West Coast to sell. Hubbard had a different idea, writing to the U.S. Navy requesting permission to undertake a world cruise. Parsons attempted to recover his money by obtaining an injunction to prevent Hubbard and Sara leaving the country or disposing of the remnants of his assets, but ultimately only received a $2,900 promissory note from Hubbard. Parsons returned home "shattered" and was forced to sell his mansion.
On August 10, 1946, Hubbard married Sara, though he was still married to his first wife Polly. Hubbard resumed his fiction writing to supplement his small disability allowance. In August 1947, Hubbard returned to the pages of Astounding with a serialized novel "The End is Not Yet", about a young nuclear physicist who tries to stop a world takeover by building a new philosophical system. In October 1947, the magazine began serializing Ole Doc Methuselah, the first in a series about the "Soldiers of Light", supremely skilled, extremely long-lived physicians. In February and March 1950, Campbell's Astounding serialized the Hubbard novel To the Stars about a young engineer on an interstellar trading starship who learns that months aboard ship amounts to centuries on Earth, making the ship his only remaining home after his first voyage. During his time in California, Hubbard began acting as a sort of amateur stage hypnotist or "swami".