Pigeon droppings lie almost an inch thick in most of Building 69. It is a long red-brick storehouse,built during the Civil War. 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. Just enough sunlight breaks through a window to illuminate what looks like a film-prop chalkboard marked with an elaborate schedule. 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. 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 churchs complicated Hollywood ties and high-profile adherents like Tom Cruise,a film even loosely based on it will guarantee discussion. When Andersons crew shot for a month last year,the picture was blandly described as an untitled Western. But as Phoenix joined Amy Adams,Philip Seymour Hoffman and others in evening clothes on an antique motor yacht,it became obvious that something serious was afoot. The Master is 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 Anderson was raised in a family of nine siblings from a pair of marriages. There Will Be Blood added scope with its historical story but it remained a story about California and Californians,as if Andersonnot unlike the young Francois Truffaut were using film to examine both his own life and the lives around him. With The Master,Anderson will tell a dual tale. The first is that of a boozy Navy veteran,played by Phoenix. The second story is that of Lancaster Dodd,who is eerily referred to only as The Master or Master of Ceremonies. Played by 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 Scientologys L. Ron Hubbard. Trust me,its not about Scientology, Hoffman said last September. As The Master took shape,Anderson,its writer and director,delved into the personalities behind cults and religious and pop psychology movements with roots in California. But a glance photographs of Hubbard in the early 50s reveals a telling likeness to Hoffman,who shares the same soft features,light hair and innate theatricality. The Church of Scientology has a reputation for being dogged about policing its image. When the screenwriter and director Paul Haggis quit the church in 2009,he told The New Yorker,nine or 10 members showed up in his yard to remind him of the damage that might be caused by a prominent members resignation. Asked about the churchs awareness of The Master,Karen Pouw,a Scientology spokeswoman,said by email: Thank you very much for your inquiry. The Church only knows about the film what it has read in the press. Believers will confront a fiction that purports to tell a truth about their world,without specifically portraying them,at least by the filmmakers claim. And Andersons admirers will be asked to follow him,one layer at a time,into his next California.