Here’s the best thing I can say about “An American Affair”: that, despite unsavory hints that it’s going in that direction, it refrains from having its 13-year-old protagonist have sex with Gretchen Mol, who plays the sexy next-door neighbor with whom he’s obsessed.

OK, one other good thing: Mol herself is terrific, at once invitingly sexy and tartly out of reach, a free spirit with a sense of her own worth. She plays a character who’s got grit but also a soft side, sensitivity but a mind of her own. What she’s doing in a movie this confused is another question entirely.

“An American Affair,” directed by William Olsson from a script by Alex Metcalf, is an uncomfortable blend of a coming-of-age story badly grafted to a JFK conspiracy theory. Toss in the hard-edged parochialism of a Catholic school and you’ve got a heady stew of mismatched elements.

The central character, Adam, is played by Cameron Bright, who played the creepy kid in “Birth.” Age hasn’t diminished his creepiness; playing a 13-year-old, he looks like he’s auditioning for the remake of “The Omen 2“ or perhaps a distaff updating of “The Bad Seed.”

It’s the autumn of 1963 – and Adam lives in Georgetown, where his parents (Noah Wyle, Perrey Reeves) are political journalists covering the administration of John F. Kennedy. Adam goes to a Catholic school and is interested in girls – so what’s a boy to do when he notices that he can see his new neighbor, Catherine Caswell (Mol), from his bedroom window – and she’s walking around naked?

First, play with himself. Second, begin stalking her. Which, to a 13-year-old in Kennedy-era Washington, means following her on errands and, eventually, knocking on her door and volunteering to do chores.

Adam spends his spare time watching her with binoculars (no more nudity, alas) – which is when he catches sight of JFK himself slipping in the side door. Our little secret, she says, when Adam casually mentions what he saw.

Adam is even more inclined to be secretive when his surprisingly prissy parents discover who his new friend/employer is and caution him against spending time with her. She has, let’s say, a reputation.

She also has a jealous ex-husband (Mark Pellegrino), a CIA agent who’s apparently been using her as either a conduit or a source of information about what Kennedy is doing, at least since the Bay of Pigs. But Catherine apparently has been deemed a security risk, so she has to endure visits from the ex-hubby’s spooky boss (James Rebhorn).

“An American Affair” has the good sense not to offer details that we might actually be able to check against the historical record. Still, it implies all kinds of wild things that are best left to the fiction of Don Delillo, James Ellroy and others who have used the Kennedy assassination as a literary jumping-off point. Here, it seems more silly than sinister – and more than a little rehashed.

In “Birth,” Bright was meant to be mysterious, playing a wide-eyed schoolboy who just might be the reincarnation of Nicole Kidman’s dead husband. Here, he just seems remote – except when he seems weird and disturbing. Not that he’s given anything all that outrageous to do; it’s just that he too often seems to have to work at acting like a human kid.

Mol, on the other hand, has a life force that practically lights up the theater. She seems too smart, too rueful and too plugged in to be caught up in the kind of shadowy plotting this movie forces her into.

The poster shows Mol wrapped only in an American flag, looking purposely Marilyn Monroe-like. Innocence isn’t so much lost in  “An American Affair” as it is buried under a landslide of ham-handed symbols and convenient plotting.

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