If you look for it, Scientology is there. But for once the publicity-wranglers were right: The Master is not Paul Thomas Anderson’s “Scientology movie.” It’s tenable to go with the writer-director’s own description of his follow-up to the Oscar-nominated There Will Be Blood. The founder of Scientology, L. Ron Hubbard, is the target here, and the religion that his cinematic stand-in concocts may have shades of non-Scientologists’ favorite punching bag, but it’s not quite the cultlike creed itself. Then again, not many other religions have devotees who quite seriously say things such as, “This is something you do for a billion years or not at all.”

But let’s back up. The story begins—slowly—with the introduction of Freddie Quell (Joaquin Phoenix), a Navy veteran who leaves the service in 1950 with a hair-trigger temper and likely a case of post-traumatic stress disorder. He’s a drunk who prefers to make his own hooch, and one day wakes up on a boat belonging to Lancaster Dodd (Philip Seymour Hoffman). Dodd loves Freddie’s “remarkable potion” and requests that he make more but, more importantly, wants to indoctrinate him into his weird group of friends.

To do this, Dodd has him undergo “processing.” Processing involves exercises such as withstanding a series of repetitive questions. (“Have you ever killed someone?” “No.” “Have you ever killed someone?” “No.” “Have you ever killed someone?” “Yes.”) Or walking back and forth—all day—between a window and a wall, describing each until Freddie starts to get angry and then delusional, imagining he’s feeling all sorts of things that aren’t there. It’s bizarre, and the reasoning behind these activities is never explained.

That’s The Master’s biggest failing. Anderson’s latest is, as expected, expertly crafted and acted. Barring its leisurely start, the pace is lullingly compelling, with almost no music adorning the odd, somewhat tense scenes between Dodd and Freddie or Freddie’s frequent outbursts of violence. No scene lasts longer than it should; the flow is smooth. Phoenix is terrific and terrifying as Freddie, walking with shoulders hunched slightly forward and his face forever screwed up tight, necessitating that he talk out of one side of his mouth. His inner anger is reflected in his outer contortions.

Hoffman, meanwhile, is the opposite, a welcoming bear of a man as Dodd, who must be charismatic to cajole so many into following him. That is, until he’s questioned: When someone challenges Dodd’s claims that his belief system can cure leukemia, Dodd calls the man a “pig fuck”; an admirer (Laura Dern in a cameo) who wants to discuss differences in Dodd’s theories at a book-release event is allotted a few niceties before Dodd barks, “What do you want?”

But the crux of The Master’s story is the relationship between Freddie and Dodd, and that means there’s not enough story to go around. Why Dodd takes an interest in Freddie is a mystery, as is Freddie’s willingness to be put through ridiculous exercises—for what, exactly?—when he otherwise knocks out anyone who looks at him wrong. If you dig deeply enough, there’s a subtext of the conflict between a person’s desire for independence versus wanting to be led, but being led never seems to be Freddie’s motivation here. If history is correct, strong personalities can be brainwashed, but, again, Freddie never appears to lose sight of who he is, even if who he is is a directionless fuck-up.

Dodd is revealed in the final scenes to be a nasty, vengeful bastard; however, that’s not quite enough to merit the film. You’re left thinking, “What’s the point?”—and perhaps wishing that Anderson had aimed for a Scientology movie after all.