Different ending idea
This is one possible theory of what the heck is up with Weaver and the brainwashed Henleys at the end. The basic setting:
1. The most likely explanation is that the locals at Weaver were mutated by the radiation from the neutron bomb, like in The Hills Have Eyes etc. They set traps all over, like the one Patty fell into, which explains how Ethan disappeared- there was some kind of self-closing trapdoor in the sand, and he fell into it.
2. The local townsfolk seem to be aware of the mutants. Maybe they have an agreement, like the townspeople don’t tell anyone about the mutants. They also work with the mutants, sacrificing people like the old guy in the jail and lure in the tourists. Strange thing is, even if they have some agreement with the mutants, why don’t they seem puzzled or alarmed seeing zombified tourists come back from Weaver and joining them like locals?
3. Three more things this doesn’t explain are the brainwashed Henleys, the sand storm at the end and how even though Jim and Ethan walked in a straight line away from Weaver, they ended up circling back. It is so tempting to reach for an alien or Indian burial ground or evil entity explanation, like in Stephen King’s Desperation. In King’s universe there are creatures that can copy humans like in The Outsider, but there doesn’t seem to be enough or ominous supernatural influence in the movie.
It is also kinda far fetched to combine mutants and an evil entity, plus the latter was never explored. So let’s try an explanation grounded in logic within the movie’s plot points:
1. Like - this is just an idea - what if when you stay in Weaver long enough, the radiation poisoning that still lingers, even in the tiniest amount, mutates your DNA, ever so slowly, until you forget all identity of who you are, and become zombified? There has been proof of long-term effects of nuclear fallout like people getting sick in Hiroshima decades after the bombing, and we could theorize that in the movie the government was testing newfangled bombs that caused more serious radiation that lingered longer and caused terrible mutations.
2. This would explain the brainwashed Henleys (like how the boys were playing basketball with no net, how the girl was listening to a walkman with the headphone wire cut off), why the townsfolk don’t seem surprised to see the tourists settling in there because they are not evil or alien copies of the tourists, and why Jim and Ethan ended up circling back - their minds weren’t thinking straight anymore.
3. What this idea leaves unexplained is the sandstorm and how the locals in Two Wells aren’t affected by the radiation. Maybe the sandstorm was just that, unrelated and a normal desert sandstorm, and maybe, the lingering radiation doesn’t reach the town. As for the occult symbols - maybe the mutants developed their own religion of sorts so they could keep going, to believe in something?