I think it was a tragedy of errors. I think I have a scenario that satisfies all of the evidence.
I think JAR paid someone to kidnap JonBenet (Michael Helgoth and an accomplice) and get his suitcase where he had stored the blanket with his semen on it (and a hair, possibly pubic) and his Dr. Seuss book, "The Seven Lady Godivas." This is the suitcase with its contents found under the open window. Someone was molesting her and I don't think it was her father. I think JAR used the book to seduce JB and that because of all the recent visits to the doctor regarding her vaginal distress, the whole sordid facts were about to be discussed and he needed to take action. A dictionary in the house was turned to the word "incest" with a fold in the paper making a V that pointed directly to that word. I've read that JAR had approached a few people about kidnapping JonBenet and also that he was obsessed with her. And also that Michael Helgoth's neighbor and friend had said that Michael had said that he was going to come into about $60,000 after Christmas, etc. That interview is on Youtube. Also, MH supposedly committed suicide (looks like a murder though) after the police interview where they had said they were coming after the JonBenet murderer. Also, someone said they thought they saw JAR walking down the street toward the house Christmas day and Michael is of similar build. So I think they came in through the door while the family was out and waited in JAR's room. The Ramsey's came home and put the kids to bed. Burke and Jonbenet got up right after that and went down to play with toys. Jonbenet took a bite of pineapple from Burke's bowl. They both went back to bed. The intruders crept into her room, picked her up asleep where she had already wet the bed. They left a ransom note (NOT THE RANSOM NOTE) requesting $118,000 somewhere in the house. This is the money that they were going to make from doing this. I remember reading that JAR had said something about $118,000 not being much money and that even he could come up with that and I think he said that to let the intruders know they would still get paid. The intruders took her downstairs with the suitcase. They tried to put her in the suitcase and she didn't fit (I thought I read that some of her fibers were found in the suitcase). She wakes up and screams. Neighbors say they heard a scream and I think that's when they hit her on the head with the flashlight to quiet her quickly. On youtube I saw one detective demonstrate that through some pipes a scream from in the basement could be heard both upstairs in the Ramsey master bedroom and across the street at the neighbors. The neighbor also claims he heard something like metal scrapping after the scream. They couldn't get the suitcase through the window, so they used it to stand on to get out and ran thinking JonBenet was dead. NEXT, Patsy hears the scream. She had gone to bed with her makeup on and she put on the clothes she had on the day before really fast and ran down to the basement not seeing any ransom note. John said he had taken something to help him sleep, so he didn't hear anything. Patsy sees JonBenet. She pokes her with the train tracks to see if she is alive. She thinks Burke did it, because she knows that they got back up and were together playing with toys and because she remembers when Burke hit her with a golf club, etc. She stages the body to look like a pedophile attack gone wrong (Patsy's clothes fibers are all over the garrot knot) and puts the body in the wine cellar part of the basement. Then she sees the real ransom note. She realizes Burke didn't do it, but the note implicates the family in some bad light--maybe for allowing the incest to continue or a promise to reveal other family secrets like drugs or who knows what if she calls the police. She realizes JAR is behind the attempted kidnapping-turned-accidental murder. She thinks she can continue with the kidnapping scenario, but without implicating the family. She rewrites the note. She wakes John. They call the police. Burke is there when the call is made and can be heard on the 911 tape. They send him back to bed. During the time that John disappeared for a while, while the police were there still thinking it was a kidnapping for ransom, John has suspicions about Patsy having written the note. John thinks Patsy killed JonBenet. There's a book that was by John's bed about staging a crime scene. During the time that John disappears for a few hours, he was reading that book and confirming his suspicions about Patsy accidentally murdering JonBenet and staging the scene. Later John "finds" the body. There's a comment somewhere that John told his two other children that the body was found at 11 am, but he doesn't "find" it for the police until 1 pm, so he did find the body and knew about it for two hours before bringing it upstairs and allowing Patsy to hang on to the body to contaminate the evidence further.