We're thrown into the middle of a situation without any information about it: the TV news says two men have abducted a young boy, and we see the boy (Jaeden Lieberher) and the men (Michael Shannon and Joel Edgerton), but it doesn't seem like a kidnapping. They're definitely on the run from the law - driving at night (sometimes with lights off and night vision goggles). We see a very weird church in which the parishioners recite a sequence of numbers back to the preacher before the FBI comes in and takes them all away - apparently the boy was a member of the church, and his speech has become their gospel. And now the boy's father has "kidnapped" him. We learn that the boy wears goggles because he's very sensitive to light and weird things sometimes happen around him.
The movie is more about "what would you do for your child" than the science fiction elements involved, but even that thread is made murky by the SF twist. And some things become clear when we reach the end, but both the person I watched this with and myself found the movie unsatisfying because it abandoned three out of four main characters to a thoroughly crappy fate with almost no explanation. It's well done, but ... yeah, "unsatisfying" covers it pretty well.