Even at his best (1993's "Totally F***ed Up," 1995's "The Doom Generation"), fiercely independent filmmaker Gregg Araki has been known to paint his cinematic works with broad strokes. Certainly capable of casting attractive actors and using them to their most physically carnal abilities, Araki's serious messages have threatened to, in the past, be cheapened by over-the-top, exaggerated moments that don't fit with his otherwise darkly realistic tone. Those days finally behind him, Araki has arrived at a major turning point in his directorial career with "Mysterious Skin," an altogether more startlingly mature work than anything else he has done. Araki's remaining signs of amateurishness—less-than-fluid scene transitions, a few awkward lines of dialogue—have shrunk to almost being beside the point, not making any lasting imprint on this sad and multilayered film's cumulative emotional strength.

Detailing the diverse lives and paths of two teenage boys living in a small Kansas town who, through a shared experience from their childhoods, are unknowingly connected, writer-director Gregg Araki (adapting from a novel by Scott Heim) takes a hard and unflinching look at child molestation and the long-lasting effects it can have on the victims. As far as motion pictures go on such a touchy subject matter, "Mysterious Skin" may be one of the very best and most real, avoiding TV-level docudrama theatrics and never shrinking away from the large and small details on the topic. The movie is free of manipulation and the obvious, going so far as to suggest that, while shaping negatively who Neil (Joseph Gordon-Levitt) ultimately becomes, he actually enjoyed the sexual relationship he experienced as an 8-year-old. The perpetrator in question, his Little League coach (Bill Sage), seems fun enough to be around, describing him as his star player on the team, and Neil, already recognizing his attraction to men, goes along with his advances. Neil savors the attention, after all, what with an absent father and a mother (Elisabeth Shue) who is deeply caring, but always working to make ends meet and, thus, uninvoled in her son's life. Now eighteen, Neil uses his brooding sex appeal to become a street hustler, an increasingly dangerous profession that leads him down roads he never expected.

Meanwhile, the same-aged, more introverted Brian (Brady Corbett) is obsessed with aliens, having experienced a close encounter with his mom and older sister as a child and being plagued by dreams that have him believing he was once abducted. How else to explain his blackouts, the missing time during assumed consciousness, and bloody noses? While his terminally cheerful mother (Lisa Long) humors his interests, Brian seeks the guidance of Avalyn (Mary Lynn Rajskub), an offbeat nearby woman who also claims to have been abducted. As Avalyn assures him his memories are slowly coming back and encourages that he continue to seek answers from his subconscious, Brian is eventually drawn to vague recollections of his own Little League team and, more precisely, Neil, a total stranger.

Using the alien angle—something he similarly did in 1997's "Nowhere"—as a smart, effectively-handled metaphor for deep-seated childhood traumas and repressed memories, a sense of the unknown washes over "Mysterious Skin" like a a pall of dread. Neither Neil nor Brian knows the other, and are as different as night and day, but when they finally end up face to face at the end, connecting in unforessen ways, they have arrived at a place of mutual catharsis. Each of them being the crucial missing puzzle piece the other has been searching for to lay to rest their disturbing experiences, "Mysterious Skin" conclusively uncovers itself to be a story whose open-ended last scene symbolizes great hope and the limitless capabilities of humanity. Until then, though, the film is as dark and despairing as it is unforcedly funny. Said humor evolves naturally, whether it be out of a particular situation or character trait, and raises its power by being a movie that feels authentic, capturing the nuances just right of small hole-in-the-wall towns and different gay lifestyles.

When things take a turn for the quietly melancholic or the stakes are raised to highly charged levels, "Mysterious Skin" sizzles with the unpredictabilities of life. Scene after scene achieves a depth that turns its back on convention, but not on narrative validity. A sequence like the one in which Neil is picked up by an older gentleman (Billy Drago) who turns out to be suffering from AIDS and searching for a connection not involving, but equating to, sex, is resplendently beautiful and agonizing. Seeing with his own eyes the possibly pitch-black effects of one's loose sexual ways, Neil is understandably shaken, but his attempts at leading a legit life in New York City with platonic soul mate Wendy (Michelle Trachtenberg) and knocking what has become a moneymaking habit aren't as easy as anticipated. His fate comes to a head in a frighteningly stark and honest scene in which Neil picks the wrong guy's car to get into. Other moments are just as sublime, including a portrayal of pedophilia that is disturbing because of what it does not do, which is to demonize the guilty party. By humanizing the coach, treating him like a smooth-talking regular guy with a hesitant undercurrent, he becomes a real-seeming person, flawed and criminal, to be sure, but someone whom it is easy to see why Neil would willingly be seduced by. Director Gregg Araki shoots these delicate scenes with honest bravery that dodges cheap exploitation, and the performances by Bill Sage (2001's "Glitter"), as the coach, and Chase Ellison, as the young Neil, are purely riveting. Araki's view of Neil, seeing him as an already sexually aware person at the age of eight, further encapsulates and cements the choices he makes as a teen, selling himself for money and confusing the attention of strange men with intimate satisfaction.

As the teenage Neil, Joseph Gordon-Levitt (1999's "10 Things I Hate About You"), sheds his image, best known for the harmless sitcom "Third Rock from the Sun," and is a revelation. This is the kind of role and the sort of powerfully assured performance that, with the right amount of attention from audiences, could be his career breakthrough. Gordon-Levitt is never less than fully convincing, and the journey he takes toward eventually coming to terms with his past is devastating. The rest of the actors give strong support to what is Gordon-Levitt's film all the way. Brady Corbett (2003's "Thirteen") is appropriately awkward and internally guarded as the confused Brian, who is certain that beings from beyond are targeting him. As friends Wendy and Eric—who are both in love with Neil though refreshingly nothing comes of this fact—Michelle Trachtenberg, breaking free from the G-rated "Ice Princess" and playing a character unlike any she has taken on before, and Jeff Licon are a worldly, likable match for the more hardened Neil. Mary Lynn Rajskub (2003's "Legally Blonde 2: Red, White & Blonde") is wonderfully real as the lonely Avalyn, whose sharing of chemistry with Brian is cut short by a rash decision that puts her at arm's length from him. And finally, Elisabeth Shue (2005's "Hide and Seek") hits all the right notes as Neil's mom, a woman whose love for her son almost makes up for her ignorance of who he has become.

"Mysterious Skin," a film whose layers of storytelling depth and character dimension could easily warrant another seven paragraphs of written discussion, is a lot of things. Sexy without pandering, profound without trying to be, amusing when need be, and unforgettably emotional the whole way through, "Mysterious Skin," like Gus Van Sant's amazing "Elephant" before it, avoids easy answers and pat conclusions. Writer-director Araki, with a more naturalistic hand in check, sees things as life really is, rather than the oversimplified black-and-white version of what some people narrow-mindedly fool themselves into thinking it is. With the end comes the sense that a lot of work still needs to be done on both Neil's and Brian's parts if they ever hope to completely recover, but the necessary first steps have been taken toward that difficult process of dealing, coping and letting go of the past. "Mysterious Skin," for all of its depictions of atrocities and human sadness, is a rarified thing of vulnerable beauty.