Hubbard attended George Washington University, Washington, D.C. (1930–32), but left to pursue other interests without completing his degree. He married in 1933 and settled down to a career as a writer. His writing spanned various genres—from westerns to horror and science fiction—and he was a popular contributor to pulp magazines. Hubbard had also developed an interest in exploring. In 1940 he was elected to the Explorer's Club and during the winter of 1940–41 was awarded his licenses as a Master of Steam and Motor Vessels and Master of Sail Vessels; ships would later play a critical role in the operation of the Scientology church.

During World War II Hubbard served in naval intelligence in Australia and aboard several vessels off the U.S. coast. Hubbard ended the war as a patient at Oak Knoll Naval Hospital in Oakland, California, apparently suffering from several war-related ailments, and it was during his hospital stay that he gave systematic consideration to his earlier ruminations on the human problem. After the war he began a personal quest for a “science of the mind.” His initial conclusions appeared in The Original Thesis (1948), prior to a more mature presentation in Dianetics. These and Hubbard's other Scientology writings, both published and unpublished, are considered scriptures by the church.

Like many thinkers before him, Hubbard believed that the basic principle of human existence is survival. Even before the publication of Dianetics, Hubbard wrote, “I suddenly realized that survival was the pin on which you could hang the rest of this with adequate and ample proof…【and】 that life, all life, is trying to survive.” Actions that support survival are good and yield pleasure, he argued; countersurvival actions are destructive and perpetuate negative states. Each individual, he believed, possesses a mind that under normal conditions operates analytically to make survival-oriented judgments. However, when the mind is not fully functioning, a part of it, the reactive mind, takes over. It stores images of experiences, called engrams, which contain not only strong negative emotional content but also unrelated elements of the experience. A later encounter with these unrelated elements may bring forth negative emotional reactions from the stored engram and lead to countersurvival actions.

To help people bring engrams to their consciousness, confront them, and thereby eliminate them, Hubbard developed auditing, a one-on-one counseling process in which a counselor, or auditor, facilitates individuals' handling of their engrams. A key aspect of this process is use of an E-meter, an instrument that measures the strength of a small electrical current that passes through the body of the person undergoing auditing. According to church teachings, E-meter readings indicate changes in emotional states that allow the identification of stored engrams. In Dianetics the goal was to rid the mind of engrams, and individuals were said to have reached a major goal when they became “Clear.”

What pushed Hubbard from Dianetics to Scientology was his understanding, among other things, of the experience of “exteriorization,” the separation of individual consciousness from the body. This experience allowed him to see the spiritual self, the thetan, as the true self that can exist apart from the body. He also came to believe that thetans had inhabited other bodies before their present one, a concept not unlike that of reincarnation in Eastern religions. The new focus on the thetan led Hubbard to postulate a comprehensive vision of the cosmos that had much in common with Eastern faiths and closely resembled the western Gnostic (Gnosticism) tradition.

Hubbard suggested that thetans had originated billions of years ago with the original Cause, whose entire purpose was the creation of effect. Thetans emerged early in the process of creation, and their interaction led to the creation of MEST (matter, energy, space, and time), thus making the visible universe possible. Over time, the thetans fell into MEST and were trapped. Eventually, the thetans experienced events that stripped them of both their creative abilities and the memories of who they were. Their movements through the MEST universe eventually brought them to earth.

The church asserts that, through Scientology training, its members come to understand both themselves as spiritual beings and engrams as energy clusters that inhibit the thetan from functioning freely. For Hubbard, the process of freeing the individual is the fundamental purpose of religion. “For countless ages,” he wrote, “a goal of religion has been the salvage of the human spirit. Man has tried by many practices to find the pathway to salvation. He has held the imperishable hope that someday in some way he would be free.” Consequently, the most sacred teachings of Scientology (the Operating Thetan, or OT, levels) are concerned with assisting the individual to operate as a fully conscious and functioning thetan.

The individual Scientologist is also encouraged to develop a more inclusive worldview by identifying with ever larger realities, or “dynamics.” At the earliest stage, the individual experiences the urge to survive as an individual first but then learns to identify with three other dynamics—the family, the tribe or nation, and all humankind. These first four realms of survival were expanded in Scientology to include four greater units—the entire animal kingdom, the physical universe of MEST, the spiritual universe, and finally infinity or God. These eight dynamics of survival are symbolized in the eight-pointed cross of the Scientology movement.

According to the church, as individual Scientologists become aware of the four higher dynamics and experience God, they are free to reach their own conclusions as to God's nature. But this freedom does not mean that belief in God is irrelevant or unimportant. As Hubbard argued, “No culture in the history of the world, save the thoroughly depraved ones, has failed to affirm the existence of a Supreme Being. It is an empirical observation that men without a strong and lasting faith in a Supreme Being are less capable, less ethical and less valuable to themselves and society.” Nonetheless, the church does not prescribe specific teachings about God but instead concentrates on helping its members to realize their inherent spiritual essence and abilities.

Scientology operates through its churches and missions. They are locally governed, autonomous corporations licensed to use Scientology materials, to teach the basic tenets of the faith, to conduct auditing procedures, and to help individuals reach the state of Clear. Any church member who has attained this state and wishes to become an Operating Thetan can attend one of the Advanced Organization centres at which training for the OT-I–V levels is made available.

Hubbard, who had headed the church, resigned all offices in 1966 and for a time concentrated on the development of the post-Clear, OT levels. Much of this research was done aboard a seagoing vessel, the Apollo. During this period, Hubbard also formed a fraternity of dedicated church members who were entrusted with the most advanced teachings of Scientology.

The Flag Service Organization in Clearwater, Florida, is responsible for providing instruction for OT levels VI and VII. The related Flag Ship Service Organization, located aboard the ship Freewinds, provides OT-VIII training. Knowledge of the exact content of the OT-level training is not freely available but is restricted to church members who undergo the training. OT-level training is reserved for those who are concerned with ridding themselves of the engrams acquired through the millennia and who perfect their abilities as Operating Thetans.

Providing oversight of the local Scientology churches and organizations is the Church of Scientology International (CSI), which coordinates the activities of the movement and promotes the church internationally. The Religious Technology Center (RTC) has ultimate ecclesiastical authority for the teachings of Scientology, owns all the movement's trademarks, and grants the churches and organizations their licenses. The RTC is also charged with ensuring that the church's procedures are followed fully and that its “spiritual technology” is properly used.

Scientology has long been embroiled in controversy. When Dianetics was introduced as a “mental therapy,” physicians and psychiatrists accused the church of practicing medicine without a license. Church leaders in turn charged psychiatry with denying the spiritual side of man's nature. Thus began a long-term conflict with the medical and psychiatric establishment, especially the American Psychiatric Association (APA), which centred upon the church's opposition to the use of any consciousness-altering drugs and to procedures such as lobotomies. Conflict with the APA, including a crusade against the popular drug Prozac, has been pursued by the church's Citizens Commission on Human Rights.

In 1958 the Internal Revenue Service (IRS) began revoking the tax-exempt status of individual Scientology churches for, among other reasons, their practice of selling counseling courses. While the church dealt with IRS questions, agents of the Food and Drug Administration raided the church in Washington, D.C., in 1963 and seized its E-meters on the grounds that they were unauthorized devices for the diagnosis and treatment of disease. These actions by the U.S. government brought attention to the church in both Australia and the United Kingdom, where government agencies also moved against it.

In response to these attacks, the church created the Guardian's Office in 1966 and assigned it the task of vigorously defending the church. It brought legal actions against publications it deemed libelous, and in the 1970s it launched an extensive intelligence operation to gather information about attacks on the church around the world. Reportedly frustrated at the lack of response to requests under the Freedom of Information Act for documents from the U.S. government, some leaders in the Guardian's Office approved a plan to infiltrate various government agencies in the United States. As a consequence of this plan, agents of the Guardian's Office were arrested in 1979. According to the church, these agents had violated church policy; they had also committed several illegal acts for which they were tried and convicted. These events alerted church leaders to problems in the office, and, following a widespread investigation, several people associated with it were fired or expelled from the church and the office was disbanded.

Over the years the church has argued many cases in court. In 1993 it won its fight for tax-exempt status with the IRS, thus ending the longest investigation in IRS history. The church saw this as vindication of the many criticisms it has faced over the years, including charges of financial mismanagement.

Nevertheless, problems remain for Scientology. Several former members have become intense critics of the church, charging it with financial fraud, illegal practice of medicine, harassment of journalists critical of the church, and vindictive actions against its former members. Scientology is under special scrutiny in France and Germany, the two countries most affected by contemporary anticult activity fueled by the murder-suicides in 1994 of 53 members of the Order of the Solar Temple, a French-speaking group that believed in an imminent apocalypse. Former Scientologists have taken their cause to the Internet, not only attacking the church but also posting copyrighted material on their Web sites. Especially harmful in the eyes of the church has been the posting of instructional materials for the OT levels, which are considered confidential sacred scripture.

In the 1970s the Church of Scientology spread across Europe and began translating Hubbard's writings into many languages. Its growth continued through the 1980s, and, following the fall of the Berlin Wall, it quickly spread into eastern Europe. Today the Church of Scientology remains a subject of controversy but operates in more than 150 countries.