I’ll try to not be too specific for the sake of anonymity. I’m a STEM PhD student at one of the top-15 universities in the US. My own advisor said that I did great academically and made good progress on a hard research project. I also passed my candidacy. But my project turned out to be pretty unrealistic, and on top of that, I had a lot of personal issues that were out of my control. Because of that, while my research progress was fine, my performance was chaotic in terms of making quality presentations for regular reports (for my advisor) and meeting deadlines. I was also kind of a lone wolf in terms of how I worked: I still talked to people and asked for advice from other lab members as well as helped them whenever they needed help, but I guess that’s not the impression my advisor got since he only saw a small part of of it all.
Anyway, I’m applying to other PhD programs now, and he already submitted his letter to like 75% of the schools I was gonna apply to. One professor from a school outside the US was so shocked by the letter, he actually reached out to me and warned me. Apparently, the letter says that my advisor kicked me out, briefly mentions that I’m “smart and hard-working”, and then, goes on to list all my flaws and ends up saying that “I might deserve a chance to try my luck at PhD at least somewhere” and that my advisor “has reservations”. That’s shocking because he told me he’d focus on the positives and that he never writes negative rec letters. It sounded like it would be mediocre or even mildly good, but this is downright horrible. The letter doesn’t even say he actually recommends me, so I guess technically, it’s not even a recommendation. That can’t be ethical, can it? I’m not from the US, so maybe, I’m mistaken.
The other letters are definitely supposed to be superb. What do I do now? Do I just ask someone else to write a rec letter? Is an absence of a letter from my advisor worse than a letter like this from him? Is there a way to fix those applications that already has his letter? Sorry for the typos - I’m kinda shaken right now.
P.S. If I exclude his recommendation after he submitted the letter, will it work (if the app portal allows it)? Is it a good idea?
P.P.S. I already got rejected from one program by the way despite me having multiple papers and stuff. It’s probably because of the letter.
Edit 1: I was kicked out from the group, not the program. I'm still technically working in his group unofficially (on a new research avenue that I had proposed an that he agreed was a good idea) to get at least one paper out of it. But I'm still officially a PhD student. But all the other labs at this university are either not working in my subfield, or they are full. That's why I'm leaving the program on my own terms (technically) and applying elsewhere. I should have specified it, sorry.
Edit 2: I asked "Will this be a bad, medium level or good rec letter", and he said "Well, I don't write negative rec letters. I'll focus on the positives because no one is arguing that you're smart and hard-working and all that, but I'll have to mention why you're leaving if they ask". To me, that sounded like it would be a mediocre letter at worst and a pretty good one at best. If I hadn't asked, I wouldn't have doubts about the ethics of it all. I just expected him to be a bit more upfront. Normally, people refuse to write rec letters if they cant write strong ones. This one isn't even mediocre...
Edit 3: He was super friendly to me, so I don't think I made an enemy. And if I did, I didn't even know that.