I'm also stuck in a difficult situation with graduate schools. My research advisor did not get his grant funding and as a result, I had to work unpaid in his lab for the entire summer. We were then told at the end of the summer that the department was in such debt that we could no longer order any more materials for research. On one Saturday, I discovered that this guy that I had met casually once (never dated and barely knew him) had apparently been stalking me because he found out the room number and building where I worked, broke in, and left a note on my desk. I was beyond terrified and I told my advisor before the fall semester started that I was scared to work in the lab until measures were taken to change the locks and to get a restraining order. He proceeded to yell at me and tell me that I was overreacting and that I needed to just get back into the lab and start performing more experiments. I asked for a week off to get proper documentation for the restraining order and to consider whether I should take a semester off, and within that time, he sent me emails harassing me about how I needed to come back and wash the glassware and how I was being irresponsible as a graduate student in neglecting my duties (Keeping in mind that I was working for free with limited supplies and resources for the past three months). It just got to the point where I decided to leave the program for good, because I didn't want to work for somebody that absolutely did not care about his students. I also knew that I couldn't conduct research properly since it was unlikely that we would get funding for the upcoming years if we already had such limited resources.
Now I am reapplying to graduate schools, and the majority of the programs want a recommendation letter from my advisor. From the tone of these requests, it seems like they are concerned that I got kicked out of the program and they don't really believe that I voluntarily left the program. However, I don't think my advisor will give me a good recommendation given the circumstances. Is it better to just not ask him for the letter and hope that some graduate school will accept me based on my explanation in my SOP? Or should I try to ask him and hope that he'll be considerate enough to give me a good recommendation?