Needless to say, thar be spoilers here!Basically, the flick is about an old text that predicts numerous calamities to the date, location and number. Catastrophes including, the accident that kills Cage's wife, 9/11 and of course, the End of Everything (i.e. Judgment Day, y'know like the Bible?).
The text is a string of numbers scrawled onto a piece of paper by a little girl in 1959 who is visited by a presence that causes her to hear whispers in her head that compel her to write the number string. The girl was supposed to draw a picture of what the future would be like in 50 years and place it in a time capsule.
Nick Cage's son gets the envelope containing the page when the time capsule is opened 50 years later. Cage is a scientist (astrophysicist) who has lost faith because of the tragic death of his wife and believes 'poo just happens.' - essentially that there is no God. His son however, believes his mother is in heaven. Anyway, Cage begins to notice coincidences in the number strings to actual events. He even visits some of the locations and witnesses the devastation that causes the prescribed body count. There is a particularly graphic sequence of the aftermath of a plane crash with people on fire and exploding and another of a subway car turning people into red mist - so be warned.
Ultimately, it turns out that whomever compelled the little girl to write the numbers in 1959 is now in contact with and communicating to Cage's son. Periodically these entities will show up (looking human until the end of the flick, by the way) and scare the crap out of everybody - one even has light come out of its mouth!. Cage eventually gets in contact with, Diana, the daughter of the little girl who wrote the page in 1959 and she gets drawn into the story along with her daughter (who is roughly the same age as Cage's son). The kids eventually dub these creatures as The Whisper People...
At the end of the entire number string, in the place of the number for a body count would be are the letters 'EE', which essentially translates into End of Everything or Extinction Event. The page predicts the end of the world. Cage is able to use data from a report he'd written to find out that the Extinction Event is that Sol (aka the sun) will have a 'Superflare', which will shoot out from the sun to bathe the earth in fire, destroying the ozone layer and thus all life on the planet.
But it turns out the little girl in 1959 had been interrupted and the remaining numbers in the sequence (which would give latitude and longitude coordinates) was actually scrawled into a door in the basement of the school. Cage finds the location and goes there to discover that it's the landing site for a huge alien mothership, and that the aliens intend to collect The Chosen (Close Encounters, anyone?).
Cage's son and Diana's daughter are of course chosen, but when Cage's son tries to take his dad with them, he's told Cage must stay on Earth. The human looking entities then reveal themselves in alien form and boy are they reminiscent of angels.
So essentially here, Cage as the scientist (the enemy of religion) is shunned by the 'angels' and must be Left Behind, while his son (who believes in Heaven, remember) is one of the Chosen who will be called up into the sky. The aliens take the kids and fly off in their spaceship. Cage is left on Earth to face Judgment Day with the rest of humanity, which does actually occur in the film - yes, everybody dies.
But that's not all - there is an additional scene after the apocalypse that show the spaceship setting the two children (in essence Adam & Eve) onto this plush garden-like planet (Eden) and the two run hand in hand toward the Tree of Life in the background:
So, like I said, it's a secret Christian flick...
