The story begins in 1995 with Samantha Darko aka Sam and her female friend Cory driving cross country from Virginia to California to be "dancers" (strippers is implied). Their car breaks down in a tiny desert town. The girls meet several locals including, the town stud who they hang out with, a creepy UFO loving motel clerk, a crazy war vet the town calls Iraq Jack, a very creepy minister and his crazy wife who thinks she can talk to Jesus, they also meet the town dork who has an instant crush on Sam. We also learn that a few young children around town have disappeared and Iraq jack is the main suspect. The first night in town Sam starts sleep walking and having dreams that the world will end. iraq Jack sees visions of a dead Sam in a ball gown who tells him the world will end.
Over the course of the movie, several senarios play out each resulting in the death or Sam or her friend Corey and then time rewinds itself.
At the end we discover that Iraq Jack is actually Justin Sparrow, Roberta Sparrows (Grandma Deaths) grandson and he was supposed to die after being hit by a meteorite on the night Sam arrived in town. Time rewinds, AGAIN, and now Knowing what to do to save the universe iraq Jack climbs on a windmill and lets the meteor hit and kill him. The next morning Sam wakes up and opts to get on a bus and return to Virginia leaving her friend Cory to move on without her. We also learn that the pastor and his wife are the ones abducting and killing the missing children (so they can catch them before they become sinners), but unlike the original Donnie Darko, they are never caught and the missing children all die.