A) the Hidden People were luring people into the forest via the whispers to shut down the lunar ray, and B) the crazy astronauts were killing those same people

Tethers discovers the crash site and is knocked out by an astronaut with a syringe, only to wake up in his hotel bed, safe and sound?  Weren't those astronauts killing everybody?  Was that an imaginary astronaut, like the one who delivered the note in Part 1 or Korka's list in Part 2?  Or was that whole discovery a hallucination to show Tethers where the crash was?

Tethers found the crash site and was injected with something by an astronaut, only to wake up in his bed, safe and sound?  Weren't they insane and killing everybody?  Were these imaginary astronauts like the one that delivered various messages (the note in part one, Korka's list in part two)?  If so, what caused them?  That also still doesn't explain how he got back to the hotel. 

the agents stop Tethers from taking the ray?  When he runs off, they're all standing around with their guns out not looking at him.  Were they busy with the other agents hit by the lunar ray?

why didn't the government agents stop Tethers when he disarms the beam?  When he carries it away, they're all just standing around with their guns out, not looking at him.  Were they preoccupied with the other agents hit by the Crazy Ray?

the townspeople's obsession with puzzles.  This was a major plot point in part 1, when Tethers uses a puzzle to escape from the sheriff, and it was never really addressed explicitly.  My understanding is that the Hidden People could only communicate through puzzles and thus inspired a mass puzzle obsession in the town through the whispers.  Does that fit?   

Why wasn't Tethers fired for disobeying orders and attacking fellow agents? 

Tethers lose his job for attacking fellow agents?

 ( the Hidden People were sending the missing people to shut down the lunar beam via the whispers, the crazy astronauts were killing anyone who came too close to said beam)

Like this.