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He didn't originally plan to kill her, but there was so much blood, he thought there was only one thing to do and that was to finish the job, and so he turned her over and drove the knife into her throat or maybe she fell on his knife wrong when they both fell to the floor during the struggle.
That's when he decided to rape her and put towels over her wounds at first so he wouldn't get sprayed as she desperately struggled to clear her lungs of blood. But then finally used the duvet so he wouldn't have to look at her or see her looking at him while silently pleading with him to help her...
But this is just my opinion.
The problem that nags me about any scenario where Rudy kills Meredith intentionally is his criminal history. Other then when he threatened someone with a knife after being discovered in the middle of a break-in, does he have any history at all of physical or violent behavior or battery of any kind?
I don't know, but from what I have read, the type of criminal acts that Guede was involved in tend to escalate. Few start out to become a rapist or killer, but once you get used to breaking into people's homes, and carrying a weapon to fend off anyone that might catch you in the act, you need to be ready to use that weapon if need be. I DO think that whatever happened was part of a perfect storm of sorts. As I meantioned earlier, something must have gone wrong, but it also must have been something that pushed some emotional buttons in Rudy that sent him over the edge. I mean, if he had planned to kill Meredith, there are ways that would have made much more sense than to leave her in a pool of blood with his own DNA and prints all over the place.
I think that one of two things happened:
1) She caught him there trying to escape, and she screamed and he realized she knew who he was and would tell the cops
OR
2) They had a confrontation, either from her finding him there or him trying to make a move on her, and she said something along the lines of "not until hell freezes over", which set him off.
My best guess is that he tried to get her to engage in some sexual activity, and had her from behind with the knife at her throat. But instead of submitting, she started screaming, and he stabbed her to stop the screaming. I agree with those here that have said that the scream being part of Guede's story is significant. She screamed all right, and it was so loud he had to make it stop. And he is afraid that others heard it, and will testify what time, so he had to make his story fit that.
I also agree with you that he put that Duvet over her because, after all the stress of the killing, he did not want to look at her anymore. I suspect she was already dead at that point, but if your idea is true that she was still gasping ... too disgusting to consider, and makes me have a worse opinion of Guede than I already do.
In her recently published book, Nina Burleigh describes how Rudy had some mental issues of some sort, possibly triggered by physical and emotional abuse as a child. The book talks about how he would wake up in the middle of the night, and act out strange scenarios as if he were awake, to the point where his friends did not want him to sleep over at their place anymore because it freaked them out. Rudy apparently went through some pretty harrowing stuff at an early age, like being locked in a bathroom all day while his dad was gone from the house, being abused, etc. Based on his behavior in the year or so before the murder, the results of this abuse may have started to show themselves as he reached adulthood. I don't know how much of the book is true, but it gives the impression that Rudy may have some serious issues that no one has properly diagnosed.
Unfortunately, it all resulted in the death of a young woman, and the incarceration of two innocent people.