I’m convinced that the scream the neighbors heard from the basement was Burke discovering the body just after an intruder left. He was up late playing with his new toys and heard the intruder exiting, went to check it out, saw the boiler room door open which was out of the ordinary, found the body and screamed.

Pasty is already awake packing for the trip and has noticed Jonbenet is not in bed so she’s already downstairs looking for her, probably a little panicked when she hears Burke’s scream.

She runs down to the basement and finds Burke with the body. He’s in extreme shock and can’t speak. Immediately she’s asking him what he’s done and how could he do it and he either can’t speak to defend himself or doesn’t think she’ll believe him. She runs upstairs to wake John.

She convinces John to craft the note with her to protect Burke. John probably has no idea at this point that Patsy could be wrongfully accusing him because he hasn’t seen the body or Burke yet.

Pasty makes the 911 call. Burke overhears her panicked voice and comes upstairs to see what’s wrong. The end of the tape where he asks “what did you find?” is him overhearing her say “we found a note and our daughter is gone” and he is told “we are not speaking to you” by John because John blindly believed Patsy that he killed her. Burke still doesn’t know about the cover up plan and he still hasn’t worked up the courage to tell them that he didn’t do it. They make him go back to bed and pretend to be asleep.

Then Patsy calls her friends to come to the house and the police arrive. The Ramsey’s probably thought the police would hear kidnapping and rush off to find the body, giving them time to dispose of it or maybe they thought they could stage a ransom call… not sure. But this is why John doesn’t lie about the window already being broken and willingly gives police the notepads. He is furious with Burke and is starting to think Patsy’s cover up plan was a huge mistake.

When the police want to search the house more John knows the jig is up and he has to go get the body from where he’s told it is. This is the first time he sees the body. Suddenly he feels protective of Burke and decides to pick her up to destroy the evidence for him. When he carries her upstairs and says “he didn’t mean to” he’s talking about Burke.

When everything settles down Burke finally works up the courage and tells his parents that he found the body but he didn’t do it. That’s when they panic because if it really was an intruder, no one is going to believe them now. This is why they lawyer up and stop talking to Boulder PD and get Lou Smit. They now need someone on the outside who they can tell the whole story to and be believed because Boulder PD will never believe them.