There is nothing supernatural at all and virtually everything is a result of people reacting to the Red Scythe flower.
- Some have a bad reaction to the flowers and are paralyzed (Eileen, Grandpa)
- Others have underlying mental illnesses that are exacerbated by the flowers (Jimmy Cochrane, Mom, possibly Fr. Isaac)
- The most common side effect is hallucinations. Kathy only encounters the Crimson One when she first gets in close proximity to the Red Scythe, and Day 5 is a megatrip after she whiffs a whole field of them. And by that point she had heard about "the Red Man" and everything else she encounters, meaning it could be her imagination running wild.
- Lilly's "prophecies" are just hallucinations.
- The strange messages either have mundane explanations (Dave is messing with her, as Kathy suspects) or are signs that Kathy may be developing a mental illness (hearing voices through static or other electronics is a sign of schizophrenia).