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The new film by Paul Thomas Anderson (Boogie Nights, Magnolia, There Will Be Blood) is a fascinating puzzle. It has a couple of extraordinary characterizations, a brilliantly realized evocation of post-World War II/mid-century America, a full supply of provocative subject matter, two of the best performances of the year so far, and a compelling, oddly convoluted story that seems to climax in the middle and then drift off into a perplexing array of semi-mysterious loose ends.

Advance word on the film has made much of its connections to the career of L. Ron Hubbard and the gospel of Scientology. Those connections, however indirect, comprise just one of the film’s many intriguing elements, and they’re more a matter of cultural backdrop than of any central drama. What really matters most in The Master is the complex, tumultuous relationship of two markedly different men.

Lancaster Dodd (Philip Seymour Hoffman at his most ebullient), the charismatic promoter of a cultish self-help movement called The Cause, is the Hubbard-like figure here, but he in no way takes precedence over Freddie Quell (an astonishing Joaquin Phoenix), the drifter and World War II vet whom he enlists as “protégé and guinea pig” for The Cause.

The story, such as it is, begins with Freddie’s emergence and gravitation toward Dodd’s orbit and ends with his disappearance from it. We first see Freddie as an oddly disturbed, sex-obsessed sailor in the final days of World War II, and the early sequences of the film follow him through a brief downward-bound career in post-war roguishness, escapades and failure as a department store photographer, migrant laborer, freelance womanizer and brawler, reckless alcoholic and compulsive mixer of cocktails (whose secret ingredients include paint thinner and darkroom chemicals), and stowaway on an ocean cruise that brings him to Dodd’s attention (and Dodd to ours).

Dodd seems a captivating charlatan right from the start, and he’s quick to spot Freddie as a “scoundrel.” And that, strikingly, draws the two men together and ignites the curious, revolving drama of this free-form dual portrait. The Cause provides the circumstances for their strongest connection, but the film is far less concerned with that than with the mercurial, semi-wild dynamics of the two men’s intense and profoundly serendipitous relationship.

Anderson’s script brings a fascinating array of emotional and psychological undercurrents into play with these two paradoxical characters, and adds some semi-triangular complications via Peggy (an excellent Amy Adams), Dodd’s most recent wife and a savvy true believer for The Cause. Phoenix’s brilliantly stylized performance, an inspired combination of angular expressionism and an almost feral intensity, is worth the price of admission all by itself.

And even with its deliberately fragmented story, The Master is well worth seeing for the richly layered social, psychological and historical landscapes conjured up by Anderson and his team: Mihai Malaimare Jr. (cinematography); Jonny Greenwood (music); Jack Fisk and David Crank (production design); and Mark Bridges (costumes).