Joseph Gordon-Levitt, who played Tommy, the teen much older than his years in the sitcom “3rd Rock from the Sun,” has grown into a remarkable young actor. Not long ago he gave a ferociously vibrant performance as a violent student committed to a psychiatric institution in “Manic,” a film that overall didn’t match him in quality. Now he offers another outstanding turn as Neil, a young man whose sexual recklessness can be traced back to abuse by a pedophile in his childhood. It’s a courageous, risky performance that matches his earlier promise. And yet “Mysterious Skin,” in which it’s embedded, proves even less successful a showcase than “Manic” was; indeed, as it turns out his excellence here is a nearly isolated phenomenon.

The subject of pedophilia, of course, has become more frequent in film and television ever since it’s become an increasingly prevalent concern in real-life. One need only think of the many episodes of TV crime shows that use it as a plot crux, even if the treatment there is usually perfunctory at best. On the big screen it’s fared better: both “Happiness” and “L.I.E.” have dealt with it in a way both mature and compelling. But while Gregg Araki certainly doesn’t treat the subject lightly or crudely, neither does he integrate it into a narrative that works as a whole; despite the suggestion of the title and the convoluted structure of the picture, there’s really very little mystery about what lurks beneath this “Skin.”

The central problem may well originate in the Scott Heim novel which Araki has adapted, but whatever the case his script is devised as a couple of separate stories that ultimately converge at the close. It follows two boys, Brian Lackey and Neil McCormick, from their time as eight-year old tykes on the same small-town Kansas little league team, over the course of a decade. Brian (George Webster), a timid, bespectacled lad whose mother (Lisa Long) is extremely protective and whose father (Chris Mulkey) is nearly contemptuous of the shy, reserved kid, grows up to become a nervous, rather geeky young man (Brady Corbet) who believes that his childhood blackouts and nosebleeds can be explained by only one thing–his presumed abduction, perhaps repeatedly, by aliens. This certitude leads him to make contact with Avalyn (Mary Lynn Rajskub), a crippled young woman who has her own abduction story to tell and can perhaps help him remember his experience. Meanwhile Neil (Chase Ellison), who lives alone with his promiscuous mother (Elisabeth Shue), becomes the prey of their coach (Bill Sage), who uses friendship, toys and gifts to lure the boy to become his sexual plaything. It’s perhaps not surprising that Neil grows into a free-wheeling libertine, prostituting himself to older men trolling the local parks and cavalierly indulging in drugs. Neil’s departure to join his long-time pal Deborah (Michelle Trachtenberg) in New York just happens to coincide with Brian’s efforts to find him, convinced that his old teammate holds the key to his own childhood trauma. During his absence Brian grows close to Neil’s best buddy, the gay (and goth) Eric (Jeff Licon) while both await Neil’s return for a Christmas visit, when Brian hopes he’ll provide the answers to his questions. (Hint: he does.)

Throughout all this, Gordon-Levitt scorches the screen with his portrait of a carelessly self-destructive kid; his scenes with tricks Charlie (Richard Riehle), John (John Ganun) and Zeke (Billy Drago) are remarkable. But he’s acting pretty much in a vacuum here. Apparently Araki doesn’t have much aptitude in coaxing convincing work from less experienced performers, because while Trachtenberg, Shue, Riehle, Mulkey and Drago comes off reasonably well, the remainder of the cast are decidedly amateurish. Corbet strikes a very different figure from the one he played in “Thunderbirds,” but his nerdiness seems false and calculated, while Sage appears to be creating a caricature as the libidinous coach and Licon is simply embarrassing as the flamboyant Eric. Even they, however, come off reasonably well compared to Rajskub and Long, neither of whom seems capable of reciting a single line convincingly. In their defense, it must be said that the script does them no favors; most of the dialogue has the stilted tone even the best actors would find it impossible to bring to life. Presumably Araki was striving for a black comic effect in many of the less credible sequences–a sort of soap-opera send-up effect–but he never hits the target. (To see a film that does, check out Bob Balaban’s “Parents” from 1989.) Steve Gainer’s cinematography, which too often accentuates overbright colors and an almost plastic veneer, doesn’t quite fit, either.

So “Mysterious Skin” doesn’t manage to get much beneath the surface of its provocative topic, but Gordon-Levitt compensates considerably by digging deep into the soul of his character. Whether he’s enough to justify the film as a whole, however, is doubtful.