Paul Thomas Anderson Film May Be About Scientology PIGEON droppings lie almost an inch thick in most of Building 69. It is a long red-brick storehouse, built during the Civil War and afterward in what used to be the Mare Island Naval Shipyard here. The interior is a filthy warren of tiny rooms, most empty, except for the pigeons, at least since the shipyard was decommissioned in the 1990s. But a corner on the south side has been cleaned up. There just enough sunlight breaks through a window to illuminate what looks like a film-prop chalkboard marked with an elaborate schedule. It records the coming and going of freighters that are nowhere in sight. With some imagination, and a dozen extras, this could pass for the maritime hiring hall where Freddie Quell, a drifter played by Joaquin Phoenix, looked for work back in about 1951, before stumbling through the docks of San Francisco to his much stranger destiny in a movie that is expected to be called "The Master." Clearly, Paul Thomas Anderson was here. Somewhere in Los Angeles Mr. Anderson, 41, is now finishing what will be his sixth feature film. Fiercely protective of his process, he has declined to speak publicly about the movie. But the details suggest a story inspired by the founding of Scientology, and that has provoked industry whispers. With that church's complicated Hollywood ties and high-profile adherents like Tom Cruise, a film even loosely based on it will guarantee discussion upon its release, on Oct. 12, by the Weinstein Company. Directing a movie, Mr. Anderson once told The New York Times, is only half the job. "The other 50 percent," he said, "is this gene of protectiveness and parenting and evil that safeguards your movie." That spirit still prevails. When Mr. Anderson's crew shot for a month on Mare Island last year, using the wing of an old hospital for some scenes, an empty admiral's mansion for others, the picture was blandly described as an "untitled western." Mr. Anderson avoided publicity and left few traces - other than the fake shipping schedule, perhaps - of what promises to be a notable piece of period filmmaking. But as Mr. Phoenix joined Amy Adams, Philip Seymour Hoffman and others in evening clothes on an antique motor yacht, the Potomac, which had belonged to Franklin D. Roosevelt, it became obvious that something serious was afoot. "The Master" is ambitious though not vast. It cost about $30 million, according to business associates of Mr. Anderson, who spoke on the condition of anonymity to protect their relationships. So the movie is larger, perhaps, than "There Will Be Blood," his California oil-boom drama. That film received eight Oscar nominations, including one for best picture, in 2008. "The Master" is of a piece with the Anderson oeuvre, which remained personal even as it grew. "Boogie Nights," "Magnolia" and "Punch-Drunk Love" described life in the San Fernando Valley, where Mr. Anderson was raised in a family that mingled nine siblings from a pair of marriages. He lives there still with his partner, Maya Rudolph, and their children. "Hard Eight," a first feature that grew from his work at a Sundance filmmakers lab, included a brief appearance by his father, the television personality Ernie Anderson, who also narrated a predecessor to "Boogie Nights," a short called "The Dirk Diggler Story." Though set in Las Vegas, "Hard Eight," like the other movies, was wrapped around some core California myths about the desert and its characters, and portrayed a kind of loose, defective family of drifters that seemed to replace real families that had fallen apart. "There Will Be Blood" added scope with its historical story, which is based loosely on Upton Sinclair's novel "Oil!" and an archetypal robber baron who might have been based on the real Edward L. Doheny. But it remained a story about California and Californians, as if Mr. Anderson - not unlike the young François Truffaut - were using film to examine both his own life, and, layer by layer, the lives around him. With "The Master" Mr. Anderson will tell a dual tale. The first is that of a boozy Navy veteran, played by Mr. Phoenix, who shares what Mr. Anderson's associates say are accidental similarities with the filmmaker's father, who died in 1997. The elder Anderson was a Navy vet who served in the Pacific during World War II, and, like Quell, was born about 90 years ago. The second story is that of Lancaster Dodd, who is eerily referred to in a screenplay Mr. Anderson initially wrote for Universal Pictures only as "The Master" or "Master of Ceremonies." Played by Mr. Hoffman, he is the red-haired, round-faced, charismatic founder of that most Californian of phenomena, a psychologically sophisticated, and manipulative, cult. Dodd was inspired by - though not entirely modeled on - Scientology's L. Ron Hubbard. "TRUST ME, IT'S NOT ABOUT Scientology," Mr. Hoffman told the journalist Jeffrey Wells, when asked about "The Master" at a party last September.