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And why would the person who wrote the fake ransom note feel comfortable enough to write a multiple page note with multiple drafts using the family’s own pen and paper unless they either had no intention of leaving the house after the murder or knew the family wouldn’t be surprised to find them in their house late at night? It’s very odd behavior indeed. Whoever did the cover up at least was part of the family or was so close to the family that they were welcome in the home at any hour.

Here's my theory, and it's just my non-expert outsider opinion of course. The unidentified male with no criminal history accidentally kills JonBenet while doing something he shouldn't have been doing with her. John Doe threatens to tell the police that the family let him meet, see, and/or get closer to their daughter than they should have let him, and therefore they are responsible for their daughter's death. John Doe forces Patsy to write the ransom note or he'll tell all. Out of her guilt Patsy writes the note that night and never tells anyone the identity of the killer.

There, I'm done pretending to be matlock for the day ;).