“Prisoners” is the most maddening kind of failure: an abrasively portentous thriller that, in spite of its copious flaws, manages to startle the audience a handful of times. Because director Denis Villeneuve regards screenwriter Aaron Guzikowski’s cut-and-dry kidnapping story as an ultra-serious treatise on torture, and because the superb cast (Hugh Jackman, Jake Gyllenhaal, Paul Dano, Terrence Howard, Maria Bello and Melissa Leo) clearly put in a strenuous effort, I will start with the positive.

First, Villeneuve is a pro at staging desperate chases, be they by car or foot. Early on, Gyllenhaal’s Detective Loki darts through the woods behind a row of suburban houses, in pursuit of Bob Taylor (David Dastmalchian), the latest suspect in a child abduction case. At a candlelight vigil for the two missing little girls, Loki locks eyes with the outwardly creepy Bob (his face bears an alarming resemblance to the sketched rotoscopes in “Waking Life”) and promptly, Bob flees. Loki loses Taylor and, in a truly jarring cut, ends up at a stretch of forest close to a raging highway. That scary highway returns in a riveting late scene, wherein Loki, braving a bludgeoning head-wound and blinding snowstorm, nearly kills himself and a passenger en route to the hospital.

There are only two other scenes with any staying power. In one, Villeneuve keeps burrowing into the beaten-beyond-recognition face of the film’s other prime suspect, Alex Jones (Paul Dano in his patented pale, chirping weirdo mode). Alex’s RV was parked near the girls’ houses the day of their disappearance, and he’s captured in the same RV, but Alex, who has the “IQ of a ten-year old,” isn’t divulging any details of their whereabouts, and the cops can’t find enough evidence to book him.

Hellbent on finding their daughters, neighbors Keller (Hugh Jackman) and Franklin (Terrence Howard) abduct Alex and imprison him in a conveniently abandoned house, where Keller, utterly clueless to the boy’s uselessness as an informant, thrashes him for days on end. When Franklin’s wife (Viola Davis) discovers the men’s secret and takes the bag off Alex’s head, the camera reflects her horrified point of view, as we see every blood-drenched, sunken, puffy pore of his face. Believing she can reason with Alex, she unties him, upon which he breaks a window and tries to stab the other three with a shard of glass. Like much of “Prisoners,” this is a manipulative, contradictory sequence—it seems to both support and condemn the tendency to judge a book by its cover—but visually, it’s an unquestionably searing one.

The other showstopper involves the chameleonic Melissa Leo, as Alex’s mousy aunt. It’s the umpteenth grungy role for her—she purrs in a baritone snarl, and wears pallid backwoods outfits and droopy oversized glasses—but she imbues her character’s strain of menace with such calmness and crack timing that you wish the rest of the film was half as subtle.

No such luck. “Prisoners” is a two-and-a-half hour film, and so much of that time is devoted to slamming things that you worry about the state of the actors’ fists. It’s a miracle when a scene ends without a face, a dashboard or a bathroom sink being smashed with a clenched fist or hammer. Gyllenhaal and Jackman are given the lion’s share of the smashing, and they’re such good, moody actors that it’s borderline abusive how poorly-defined their roles are here.

Loki, in particular, is a ridiculous character, inside and out. The filmmakers clearly envisioned Nicolas Cage at his most unhinged when dreaming up this guy. He’s decked out in bad-boy tattoos, and he has comically over-gelled hair that sticks out and flops all over his haunted face whenever he gets mad, becomes scared or thinks hard. If he were a dumb ex-con trying to cope with the free world, Loki would make total sense. Presented as a supposedly pensive cop, he’s merely ludicrous. He beats up the wrong people, spends countless hours mulling over arcane, symbolic clues that lead nowhere (chiefly, the maze drawings that several of the suspects leave all over their houses), while disregarding the most eye-opening clues (in a particularly dumb scene Loki uncovers trunks full of living, poisonous snakes in a suspect’s locked bedroom, then leaves the house—a house where kids might be trapped–with the snakes unloosed). Loki only seems to figure things out when they fall into his lap. You wouldn’t trust this guy to find a cat.

Then, there’s Jackman’s Keller. We care about him when he loses his daughter. We emphasize with him when the cops come up short. We even understand his need to beat answers out of Alex. But once Keller resorts to scalding the clearly brain-damaged Alex, and to outright lying to his family about developments in the kidnapping case, it’s impossible to like him. The performance is one-note anyway; Jackman has a talent for bellowing and seething, but we sense that Keller’s rage existed long before his daughter went missing, and we never see the inner workings of it.

The usually dynamic Howard, Bello and Davis are reduced to moping; these are weak, weepy characters, left on the sidelines. And given all the talent behind the camera (cinematographer Roger Deakins frequently works for the Coen Brothers), there’s a disheartening amount of hokum: abrupt fade-outs; countless shots through fogged-up windows; voice-over prayers.

In the end, “Prisoners” doesn’t have much to say beyond the tired advice several of the characters impart to each other: “Hope for the best, expect the worst.” That’s pretty slim pickings for a film that relentlessly nosedives into blood and snakes and death.