system
Given the following post, respond as if you're commenting on Reddit:
human
My former P.I/Thesis Advisor went nuclear against the whole lab, me included. Advice appreciated

Tl/dr: I can't get a rec. letter from my thesis advisor because we do not see eye to eye anymore and I don't think it is my fault that this has happened.

Roughly two years ago I joined a bioinformatics lab for my Masters, my P.I. back then was an amazing mentor, she was patient, insightful and rewarded independent thinking and proactiveness. We published four papers together and went to a few conferences, so I was pretty damn sure that I would get a good recommendation letter (especially since I was also a T.A. for her class, extra-officially).

Last year we had some drama happening in the lab, a postdoc was basically just playing computer games in lab all day and leeching off the graduate students' work, the P.I. got (understandably) mad at the whole lab and fired the dude. After that she was never really the same and got progressively worse month after month, starting to verbally abuse her students in front of the whole lab and stopped relegating the good projects to us (she would just work on them herself and publish alone or with her collaborators).

During this time I was in an internship in my dream university in the US so I thought it was just a transient thing, but as soon as I got back and told her of my desires to pursue a PhD in the US she completely "disowned" me, going so far as removing me from the lab communication group since I were "already with a foot out", in her own words. This happened a few months before my thesis defense, which she went out of her way to make as complicated to schedule as possible.

I am not going to ask her for a recommendation letter, as I have no idea if she will actually write about what we accomplished or if she will sabotage me. I know this potentially looks bad for my application as she was my thesis advisor, but is there any way I can communicate her descent into spitefulness (obviously not with those words) without making it sound like excuses? I'm pretty sure she was struggling with mental health issues and a lot of stress, and that she also probably felt betrayed for trusting so much in her students and having them stab her in the back, but it seems unfair that I should get penalized for those things.

Anyway, thank you for reading thus far, have a great day.
gpt
You have to ask her if she is comfortable writing you an strong letter. If she isn't, perhaps a former postdoc from your lab that you have a good relationship will, and will explain the situation a bit.