Jaz and Lisa Matharu are parents of their kind but severely autistic son, Raj. The family of three decides to go on a vacation in the desert area of California, but this ultimately does not turn out to be a good decision.
The Mojave desert is a large place, and for the most part, no one knows what is there, except for sand. Raj suddenly disappears, and the couple is grief-stricken. Soon enough, however, he magically reappears, unharmed and unfrightened.
However, Raj seems to act a bit differently now. The difference isn't very noticeable, but certainly something his parents would pick up on. Eventually, Jaz and Lisa find out that things like this have happened before in the desert, and the fate of the people that experienced them hasn't always ended well.
Coyote is a mythical creature and prankster, and the couple believe that he may have been the one to cause the disappearance and reappearance. While civilized people call them crazy, believers in the old myths of the desert start to reappear, and come to the area.
Gods Without Men shows the unification of all of these people, and their sudden and unexpected meeting in such an odd place. All of them try to find out what is going on and why, but they all come to practically the same conclusion - there is no real answer.