1) Teresa visits Avery Property 10/31
2) She is reported missing on 11/3
3) Colburn calls in plates 11/3
4) Car is found, without plates 11/5
Option 1) Colburn finds car and Teresa's remains off the Avery property on 11/3. He calls it in. He decides to use opportunity to frame Avery and puts the wheels in motion. (too coincidental that Teresa was at Avery's days before, killed by a third party AND found by Colburn (and or Lenk))
Option 2) Colburn is watching the Avery place (at that point in the litigation they would be on Avery 24/7 - NO QUESTION). He sees the car enter, logs in the plates but, it never leaves??? By 11/3 he enters the property from the back snooping around for the car. he finds a matching car but, it has no plates. The VIN tells him it is a '99. He calls in the pate number he logged in days before. He gets the info that it belongs to missing person but, has to use year and make to confirm it might be the car he is looking at. He is stuck because he has no warrant. They wait for the car to be found. Any Avery or Dassey could have committed the crime. If it was not Steven, the real killer framed Steven OR cops planted some info to help the case along (which is convenient AND if they can't pin it on one Avery they all walk)) Likely both the real killer and the cops planted junk independently. Brendan either saw nothing (and gave a total false confession) or agreed to the theory presented to protect a family member he had more allegiance to (not realizing he would not be making it to 6th period...). A twist on this would be that Colburn is watching the place as Teresa enters. He witnesses some amount of foul play. He takes down the plate or snaps a photo or two (getting the plate number). By 11/3 he has found the car on the Avery lot (rest is same as above).
Option 3) Again, Colburn is watching the Avery place. He follows Teresa as she leaves the Avery's. He pulls her over and kills her. He puts her in the back of the car (hence her blood being there). He removes the plates as 1) it could be reported missing at any time (and you would not want to be caught with it then), 2) placing the plates at a different location on the Avery property increases the probability something is found by searchers and 3) it makes it seem like there was and attempt by Avery to conceal the car. Colburn and Lenk burn the body at the quarry and park car on Avery lot (after doctoring it up. the lot is massive and can be accessed from the quarries). By 11/3 Colburn is in a panic. Woman went missing on 10/31 and she is not reported missing!!! He calls in the plate (oops, she was just reported missing). They continue to wait for the car to be found. They join the detectives on site after the search warrant is in place. They drop the bones in the burn areas (again, both burn areas on the property increases probability they are found). They have cleaned the key as they have used it. They put on some of Steven's DNA (from what they have is custody, wiping it on a tooth brush in the trailer...) and drop it in his room. The Prosecutor needs a theory. Brendan was there when Teresa was there. They realize he is low hanging fruit. They feed him a theory (that implicates Steven - who they want badly). He gives a false confession. Prosecutors tell the, at that point, "pro Steven Avery" world the confession. Pendulum swings in their direction. Steven Avery is the devil and all jurors are tainted. They don't even use Brendan confession in Steven's case - he is too unpredictable AND there is no blood etc. in Steven's room. Prosecution at some point changes theory (for STEVEN'S trial ONLY) that she was killed in the garage. Bullet is dropped. (If they had drained some of Teresa's blood to sprinkle around before burning her - the perfect crime!!)
The Ex has been harassing Teresa. She goes missing and he panics because there could be all kinds of messages from him on the phone. At that point he assumes he will be the prime suspect. He deletes the messages. Unless it is Option 1 above, he has nothing to do with it.
How does Steven do it? Again, Colburn is casing the place. Either he writes down the plate or takes a picture of any car that enters OR he sees some amount of suspicious activity when Teresa is there and takes notes. Steven Avery has met Teresa before and develops infatuation. Girlfriend is in jail and he knows this is the time to make a move. Before Teresa arrives he covers an area in the garage with plastic. He rapes her and shoots her in the garage. The bullet initially or eventually finds its way under the compressor (Brendan may have seen or heard something/been involved). As Steven is now overly conscious of everything he notes he is being watched. He can't take the car off the property. He burns the body (the plastic, his clothes....) in his pit (Brendan may even see some toes). He tries to move the bones to other areas to shift suspicion from him. Best he can do with the car is to try to hide it on the property (crushing it would not really do anything AND family member may note him doing it). His blood gets on the car and hers as he puts her or something involved in the crime in the back. He does not overly clean car as by then realizes he is toast (or can't spend too much time on it as he is being watched/family members may take note) but, he does hide the plates. Colburn goes snooping around, sees a Rav4 without plates that matches the car he saw and calls in the plates that he already had. He can only match the car by year and model. He can't act as he has no warrant. Somehow the key is not found in the first search (we are talking 40 acres, several buildings and almost 4,000 cars). After the first search Steven thinks it is all clear. He scrubs the key and just leaves it in his room. Prosecutors have to develop a theory. They create one and either Brendan saw noting and gives a total false confession OR he saw something/was involved and thinks confessing to the cop's version is equivalent to what actually happened and wants to please them. Prosecutors figure out their theory does not work (Teresa's blood is not in the bedroom etc.). They search the garage again and find bullet (Steven did not do a good job cleaning - he did a good job preparing). Ex cleans out VM as he thinks he could be a suspect (but is really not involved) and blood vial in evidence room was just handled sloppily over the last 20 years. The prosecution is stuck with the original theory for Brendan's trial.