M. Night Shyamalan makes movies that are not really about what you think they’re about.

I don’t mean the advertising is misleading or anything like that. I mean that while you’re watching the film, you believe it’s about something supernatural or fantastic, only to discover in the final act that it’s been building up to something else entirely, something weightier and more philosophical. The writer/director’s famous “twists” are not just in the plot, but in the whole subject matter.

“Signs” continues that trend, while building on the work Shyamalan has already done. It’s a blend of “The Sixth Sense’s” creepiness with “Unbreakable’s” deliberate pacing. Some found “Unbreakable” TOO slow; that isn’t a problem here, where the slowness is filled with anticipation and dread, not to mention finely wrought performances from Mel Gibson and Joaquin Phoenix.

Gibson plays Graham Hess, a farmer in Bucks County, Pa. A one-time minister, the death of his wife has damaged his faith beyond repair; he now pointedly asks that the townsfolk not call him “Father” anymore. He is angry at God, to the point that he denies His existence. “There is no one watching us, Merrill,” he tells his brother ruefully. “We are all alone.”

Merrill (Joaquin Phoenix) broke records as a minor-league baseball player but had an outrageous strike-out record that prevented him from making it big. He lives with Graham and Graham’s two children, Morgan (Rory Culkin) and Bo (Abigail Breslin). He considers joining the Army, just to have something worthwhile to do.

The first seconds of the film are gripping, with crisp, eerie sound and a foreboding atmosphere. (Credit Tod A. Maitland for the sound, veteran cinematographer Tak Fujimoto for the look, and Shyamalan regular James Newton Howard for the music.) Graham is awakened. Something has happened outside in the cornfield. He investigates. Crop circles — huge areas where the corn has been flattened into a strange pattern. Whether this is a hoax or a sign is the issue, at least at first. That is all I will say about the plot, and beware of anyone who wants to tell you more.

Characteristic of a Shyamalan film, there is no panic. It is surprising and perhaps amusing given what goes on here, but the characters retain a sense of calm and definitely a sense of humor. They remain people, after all — the most human of humans, with flaws and qualities and quirks.

It leads to a long, dark night of the soul for more than one person, both literally and figuratively, wrapping into a genuinely significant evolution of character. Where “Signs” is not as fine as Shyamalan’s last two films is that they worked well even on the basic level of being ghost stories or superhero tales; the twist in theme was merely the master stroke that provided the depth. Until “Signs” reaches that point in the story, it does not stand as solidly. It’s a rather ordinary UFO story — albeit an expertly staged and photographed one — and it NEEDS that added depth at the end to make it work.

It does work, though, and to fault it for being unimaginative in the supernatural department would be to miss its real point. That point is ponderous and even faith-affirming, but also very, very cool, even as it intentionally gives itself a bit of camp. A creepy good time — and perhaps a surprisingly emotional one — will be had by all.

B+ (1 hr., 46 min.; PG-13, scattered profanity, a lot of suspense and scariness.)