Front-loaded with an epic sense of foreboding, “The Good Shepherd” proposes to offer a shadow history of 20th-century America as filtered through the rise of the Central Intelligence Agency during the Cold War. It’s a sprawling task, and not only for director Robert De Niro and his A-list cast, but for the audience, too: The film is so heavy with cryptic intrigue and spy-vs.-spy doubletalk that box offices should hand out super-secret atomic decoder rings with every ticket.

That alone doesn’t make the film a chore. It’s actually a large part of its appeal. Screenwriter Eric Roth (“Munich,” “The Insider”) lays out in meticulous detail the machinations of a rarefied and ruthless core of agents and operatives who played a dizzyingly complex chess game of “Us vs. Them” (them being the KGB, mostly) in the two decades between the fall of Berlin and the Bay of Pigs fiasco in 1961.

Drawn to a significant degree from the life of American spymaster James Angleton, the narrative is cast through the unwavering prism of Edward Wilson (Matt Damon), high-born son of a defrocked naval officer, who as a child was the sole witness to his father’s suicide.

Wilson has dutifully kept dad’s farewell note sealed, the facts of the “accident” as securely tucked away as the tiny model ships he constructs in glass bottles. It is the act that shapes and defines the rest of his life. By the time Wilson follows his father’s footsteps into Yale and the secret society of Skull and Bones — that über-preppie seedbed of an Illuminati-like power elite — he’s clearly a born spook. It takes little more than a rah-rah speech from an FBI agent (Alec Baldwin, who skulks like a B-movie heavy in a fedora and trenchcoat) to persuade Wilson to expose his poetry professor (the peerless Michael Gambon), an apparent Nazi sympathizer and, perhaps worse for the 1930s, a homosexual. Soon enough, there’s a war on, and Wilson is handpicked for a job in the Office of Strategic Services (by Mr. De Niro himself, in the hammy role of a wry, diabetes-riddled warmaster named “Wild Bill” Sullivan). Thus begins the smothering of dreams and the slow death of a soul.

There’s a fat novel’s worth of exposition yet to come — skipping between continents and generations, Russian double agents, and blind alley assassinations — recounted in a profusion of flashbacks that revolve around a pivotal investigation into the security leak that sank the Bay of Pigs invasion. Wilson, master of disinformation and seamless occlusion, is a chief suspect, who in turn suspects everyone else.”Trust no one”is his motto. Paranoia is his co-pilot. His life, and that of the nascent CIA, gathers in fragments around this moment, as a grainy surveillance film clip is analyzed like a Rorschach blot for clues to the traitor’s identity.

The identity that actually remains a blur throughout “The Good Shepherd” is Wilson’s. Mr. Damon, who has ample experience in such slippery roles as “The Talented Mr. Ripley” and the post-Bondian hero of the “Bourne” thrillers, appears perfectly cast. But his character’s gray flannel heart seems unknowable, as if every human element of emotion and humor has been sucked out through a pinhole. The actor is brilliant at portraying dull, even nil. He makes Wilson’s brief, tragic flourishings to life almost painful to watch.

But the movie does exactly the same thing. Even a Friar’s Roast-worth of colorful supporting players — William Hurt, Timothy Hutton, John Turturro, Joe Pesci, Billy Crudup — fails to rouse the film from a coma-inducing pace. The plot sketches out a kind of sins-of-the-father arc across three generations (the son that Wilson neglects in his obsessive service becomes an agent, too, with catastrophic results) that implies certain fateful motivations. Unfortunately, these are never made clear enough to survive the endlessly crisscrossing subplots and switcheroos.

Worse, Mr. De Niro completely wastes Angelina Jolie, which ought to be punishable under the Patriot Act. Her vavoom is deployed early on, then abandoned. As the randy Clover, sister of Yale senior Wilson’s best friend, she seduces the shy, quiet poet into a quickie, an instant pregnancy, and the blue-blood version of a shotgun marriage. Thus must end Wilson’s romance with a spunky deaf classmate, and begin decades of loveless wedlock, which parallels his rise through the spy ranks — mostly spent abroad or at the office.

Now, it’s hard to imagine any red-blooded man (or many women, for that matter) who would not consider Ms. Jolie a fantastic consolation prize, even here in the Stepford Wife drag of a 1950s Virginia hausfrau. Yet the movie insists that Mr. Damon become a nearly neutered robot who sleeps in a separate bed! I’m not suggesting that the actress should be consigned purely to sexpot roles, only that she has been miscast in a way that torpedoes the movie’s emotional credibility.

Such choices, however, are consistent with the hermetic nature of “The Good Shepherd.” There’s a message sealed up in there somewhere, about the sons of powerful men and the blood-caked path to destiny. Timely, too, depending on your taste for conspiracy in these shaky years since the attacks of September 11. But for all its actorly gravitas and whiskey-toned cinematography, such truths remain as convoluted as the Enigma Code.