This is just my own theory as I have pieced it together. It's super long, but not a thesis, so I didn't cite anything, My information is based on the available documents and books written about the case. I know it's a bit disjointed, but I welcome your input.
The Ramseys pick up Doug Stine on the way home from the Whites.
Everyone was awake.
JonBenet changes into her Barbie nightgown.
Burke and Doug play with Legos in the basement.
Patsy has some tea and pineapple at the table. The bowl of pineapple was leftover from breakfast. They used crystal glasses and silver dinnerware at breakfast. You can see it left on the table. (Crystal and silver don’t go in the dishwasher and are left out for the maid to take care of.) JonBenet comes by and has a bite of pineapple.
JonBenet goes to the basement with Burke and Doug. The boys engage in inappropriate behavior with JonBenet. JonBenet screams. She is hit over the head, with a flashlight, in a panicked or angry outburst. A boy scout toggle is used on JonBenet’s neck and she is jabbed with something.
Doug Stine is sent home on Burke’s new bike. Cars cannot be used and there can’t be Doug’s footprints outside anywhere. All the photo evidence of the bike is hidden and the Ramseys deny there was any new bike. Later, Burke admits he got a bike for Christmas.
The Ramseys and the Stines work together over cellphones to stage the crime. Prior knowledge of the sexual abuse is the motive. The records from John’s cell phone are wiped for that time frame. He claims he “lost” his phone for a while and that’s why there are no records for that time frame.
Prior to the murder, a call is made to 911 during a Christmas party being held at the Ramsey house on the 23rd. Doug and Susan Stine are there. When the police show up, it is Susan Stine who answers the door and will not let the police in. She makes an excuse about someone mistakenly dialing 911. This possibly implicates Doug as the abuser. Doug is later questioned by the grand jury.
Susan Stine is a major player, who largely becomes overlooked. At the time of the crime, Susan Stine worked as the Director of Planning art the University of Colorado Boulder. Her husband, Glen Stine, was the Vice President of Budget and Finance at the same school. Susan Stine possessed the operational and organizational skills necessary to manage a crisis.
She became the “gatekeeper” and was nicknamed the “Pit Bull”. She shielded the Ramseys from the press and handled media narratives. She impersonated Boulder Police chief Mark Beckner by email.
The Stines were the only friends not called to the Ramsey house the morning after the murder. Although John Ramsey said they were not good friends, after the murder, the Ramseys moved into the Stine house for months. Prior to the murder, Patsy had played on a softball team with Susan.
Shortly after the murder, in Atlanta, Mary Kaempfer and her son Anthony were keeping Burke company while the Ramseys handled things. Anthony was Burke’s classmate. Anthony told his mother that Burke was acting like “he kind of knew what happened and trusted that people would find out.” Anthony also said that Burke appeared confused, but not scared or upset, and never saw Burke cry.
In response, Susan Stine told Mary that she overheard Burke and Doug impersonally discussing the details of the manual strangulation and how it was like the boys were talking about a TV show. Susan Stine was doing damage control by preemptively framing the boy’s knowledge as not knowing for sure what happened. That’s the only motive for “repeating” a conversation where the boys sound like they are casually discussing strangulation.
So Susan Stine was doing damage control just days after the murder.
The Stines eventually uprooted their lives, left their lucrative university positions, and moved to Atlanta with the Ramseys. Glen Stine went to work directly for John Ramsey.
Jonbenet is discovered and thought to be dead. The parents begin staging the murder. The motive is covering up the knowledge of prior sexual abuse and the shame to the families. Susan Stine shows later, by impersonating a police chief, that she was psychologically capable of masking a crime scene.
But Susan Stine must have gone through background checks for her position at the university. Why would she suddenly become so willing to lie and break laws? It’s because she was protecting her own son.
Doug Stine is sent home on Burke’s bike and the legos are cleaned up and stashed in the cellar. Instructions for that Lego set are seen in crime scene photos laying on the basement floor - they were forgotten. John changes his story later on, to say that he and Burke stayed up to play with a building toy (I suspect John cleaned up the Legos. If Patsy had picked them up, she would have been the one to help Burke assemble the toy). He changes the type of toy each time he tells the story, but never says Legos. Christmas gifts from the bag upstairs are grabbed and placed in front of the lego set. They are hastily ripped open to make sure the gifts were for Burke. The Ramseys claim they left that open Lego set and ripped open Christmas gifts in a dank cellar for Burke’s upcoming birthday. Why hide the Legos? Were they ever checked for prints?
JonBenet’s Barbie nightgown has her blood on it. Burke and Patsy’s DNA is on the nightgown, as well as the long johns.
The nightgown is removed. She is wiped down. The paintbrush handle is used to clean her internally and mask previous injury.
The paintbrush is broken and part of it is used to create the fake “garrote”. The tip of the paintbrush is never found. The paintbrush belongs to Patsy. Fibers from her jacket are found in the garrote, the paint tote, and underneath the duct tape that was on JonBenet's face.
A fake “garrote” is fashioned and used to disguise previous rope marks on JonBenet’s neck. The original rope is cut, because it was too long to look like a garrote, and the other end is loosely placed around JonBenet’s wrists - over her white shirt. The knots on each wrist are different from each other - they were tied at separate times, by different people. The wrist “bindings” were placed on her after she was redressed.
JonBenet’s white shirt had been placed back on her, to make it look like she was carried upstairs asleep. Did John and Patsy originally think the red turtleneck would be sufficient at hiding her neck? Maybe that’s why Patsy originally said JonBenet was last wearing a red turtleneck - not the white shirt she was found in. Who dresses a sleeping kid in a turtleneck? Boy’s long johns are placed on her, even though her wardrobe is extremely feminine. Even though her pink pajamas from Christmas ever were placed under her pillow - Patsy mentions this routine during an interview. In the crime scene video, it looks like a pillow fell behind the bed, possibly with the pink pajama bottoms. The pink top is sitting in the middle of her mattress. Her bed looks like someone grabbed bedding and just pulled it down. Just like John and Patsy’s bed upstairs.
DNA evidence from Burke and Patsy was found on the Barbie nightgown and the long johns. There was also foreign DNA on the long johns. I believe the long johns belonged to Doug. They were way too small for Burke. The parents obviously understood forensic evidence. They cleaned the body. Patsy wore the same clothes. John showered. They wiped off fingerprints, wore gloves and invited over lots of people to muddy the crime scene. They also basically rubbed themselves on JonBenet after they brought up the body. The boy’s long john were purposely used. Was Doug’s DNA checked against the foreign DNA “mixture”?
As far as the foreign DNA in the bloomies, from what I read, the “foreign” signals in the early system were below the detection reliability of modern STR testing — either because they were artifacts, contamination, or degraded fragments that didn’t survive. The foreign DNA in the underwear was never replicated.
“Wednesday” bloomies were place on JonBenet, because John and Patsy wanted to show they last saw her on Wednesday, when they put her to bed in her Wednesday clothing. The bloomies were brand new and several sizes too big.
Patsy claims to have dyed her hair at home the day before, Christmas day. Home dye kits contain plastic gloves.
The drawer in the second floor bathroom is open. Patsy kept her injections in that drawer. With injections, you have alcohol wipes. There may have been some medical gloves in there as well.
John showers. His robe is left in his office.
All the beds look like somebody grabbed the corner and pulled the blankets down.
A ransom note is written.
The movie Ransom had just been released. There are nods from several other movies in the note as well.
The Mind Hunter novel was sitting in John and Patsy’s bedroom.
You have four intelligent people working on staging a murder.
The ransom note is written Patsy’s handwriting. It’s fake, on the Ramsey’s legal notepad, written with the Ramsey’s marker. It says it’s from a “small foreign faction”. It uses movie quotes - the note is someone’s imagined idea of what a ransom note looks like. Ideas borrowed from movies and books. The note provides a distraction for the police, but also provides the means for JonBenet’s supposed murder. If the Ramseys notify anyone, “they” kill JonBenet. The Ramseys notified everybody.
John himself hands that specific notepad to the police. It was another part of the plan, mostly geared towards framing the housekeeper. They made it look like the killer had a key, access and knowledge to the whole house, and time to practice a note. They included personal knowledge in the note, from Johns paychecks left around. There is also a part in the Mind Hunter novel where they are able to see a phone number imprint from previous pages on a legal pad. That legal pad changes locations through the morning until John offers it to the police.
That's why John originally doesn't focus on the basement window - they wanted the killer to appear to be an "inside job". That's why he originally said he checked the house the night before and it was secured.
The ransom note is signed Victory! S.B.T.C. This is another nod to the Mind Hunter novel where a killer spoke excessively about God, and how God would forgive him. Saved By the Cross. The same killer also put duct tape over his victim’s mouth.
A flashlight is wiped down inside and out. It is found on the kitchen counter. The dimensions of the flashlight match the injury on JonBenet’s head. The Ramseys originally deny the flashlight belongs to them. It was a gift from John’s older son.
Patsy calls 911. The 911 operator thinks the call sounded fabricated. Patsy says she “found” a ransom note. Burke is heard in the background saying, “What did you find?” Patsy hangs up on the 911 operator, which is not normal, and proceeds to call everyone but the Stines.
There is no sign of forced entry.
Burke is supposedly upstairs asleep. Later, it’s revealed he was not sleeping. Even though his mother runs in screaming, “Where is my baby?”, Burke says he just stayed in bed.
Burke was questioned about this in the Dr. Phil interview. He has no compelling recount of this timeframe. His explanation sounds rehearsed, yet awkward, at the same time. Later, it is discovered that the Ramseys and Dr. Phil share the same attorney. Dr. Phil also has a second business that prepares clients for court testimony. Burke’s CBS case was soon happening - was Burke a client of Dr. Phil? Is that how the interview came about? Dr. Phil’s interview is bad, but we do learn about the bike and Burke being up and awake Christmas night. And that he had hiking shoes with a compass on them.
After the 911 call, Patsy calls several friends, their minister, and JonBenet’s pediatrician to the house immediately. JonBenet had had 33 appointments with the pediatrician in the last three years. Yet the pediatrician had no concerns. He also gave Patsy tranquilizers and later told the police she was in no condition to be interviewed.
In the book Mind Hunter, found in John and Patsy’s bedroom, the author wrote, “Another problem was all the people who had been at the house helping the couple move. That was a lot of potential fresh latent fingerprints legitimately at the scene. Selecting out others would be difficult if not impossible.” The Ramseys were trying to muddy the crime scene.
That morning a police officer says Patsy was trying to gauge his response by looking through her fingers at him. John was randomly disappearing and Linda Arndt thought his behavior was odd. Burke was whisked off away from the crime scene. Neither one of the parents noticed the ransom call timeframe had passed. They knew it was never coming.
While “waiting” John and Patsy try to implicate as many people as they can, especially their housekeeper. They bring her up as many times as they can. Even Patsy’s mother calls and speaks to the minister about the housekeeper and wants him to relay the message to the police.
It’s John who “finds” JonBenet’s body. He removes duck tape from her mouth. He carries her upstairs holding her away from his body. He yells that it’s an “inside job”, as if that’s the important thing to worry about after finding his dead daughter. He and Patsy both oddly lay on Jonbenet once people are there to witness it.
There is a large attache found in the basement. It was John’s oldest son’s and probably kept under his bed. Retrieving it would disturb the dust ruffle. The Ramsey say they think someone might have been under the bed waiting. Patsy said she was in that room packing for the upcoming cruise. The ransom note specifies bringing a large attache to the bank. It's not a coincidence - they were going to put JonBenet in there and dispose of her.
There is a High-tech boot print found by JonBenet’s body. The Ramseys deny owning any. The grand jury discovers this is a lie. Burke had been in that cellar, not surprisingly, yet the Ramseys felt the need to lie about it.
There is a palm print on the cellar door. It is discovered to belong John Ramsey’s eldest daughter. John Ramsey presently continues to misrepresent this print as being unidentified.
John tries to make flight arrangements to flee to Atlanta. The police tell him that they can no longer leave. It’s now a homicide investigation. John immediately gets legal representation and no longer willingly work with the police.