|I have been trying to find a new job with very little success since the end of 2020. After a lot of failed attempts. I finally landed an interview for a data science position at a startup, which I thought went very well. After the interview, they asked me for professional references, including from my current supervisor. After a very prolonged process from there, I finally learned I didn't get the job. Today I learned from a personal contact within the company that despite his assurances to me that he'd be happy to give me a positive reference, my boss failed to do so, and his equivocal endorsement was a major factor in their decision. In fact, prior to speaking with him, they'd been enthusiastic about hiring me. I'm gutted, but also very concerned this will happen again. How do I deal with a less-than-positive reference from my supervisor in future applications?
Three wall-of-text paragraphs of background follow, which can probably be skipped by anyone wanting to answer this question, but which were very therapeutic for me to write and post.
My workplace has been an extremely toxic environment for several years now, and in particular over the last two years or so my boss's behavior has become increasingly erratic and occasionally abusive, culminating in inexplicably abusive behavior directed towards his two most vulnerable employees within the last 18 months. Because of the nature of my industry (academia), there is very little recourse to seek intervention from any power structures above him. HR has had some minimal involvement, but its role is clearly to protect the reputation of our employer rather than protect employees. Beyond the normal ethical implications of this, there are certain relatively powerless groups involved (undergraduate students and nonhuman animals, specifically) that I feel a particular obligation to shield from the negative effects of his (and certain others' in our work group) behavior, and although I've done my best to maintain a positive relationship with my boss despite his behavior, it's clear I exhausted whatever social capital I had with him some time ago in trying to meet what I see as inviolable ethical responsibilities of our work.
When it finally became clear to me that I could no longer protect the vulnerable groups involved in our work, I knew that my academic career was over and it was time to find a new job. That was in late 2020, and I have been actively job searching ever since, with my boss's knowledge and apparent support. Unfortunately, due to the nature of our work, there are regular unplanned events that may occur which directly impact the medical or behavioral health and welfare of the animals in our care, which require my involvement. (Among his other issues, my boss has refused to listen to his employees repeatedly telling him that we are understaffed, and consequently I am one of only a few people, or in some cases the only person, qualified to respond to these events. I do not know what is going to happen once I leave.) These events can be extremely time-consuming as well as emotionally and physically draining for me and have significantly impacted my ability to job search, but I feel ethically obligated to respond to them nonetheless. I am desperate to get to a point in my life where this type of work is no longer my responsibility, but the work itself is impeding my ability to escape.
An added complication is that I came to my current job suffering from a significant mental health impairment (major depression, strongly career-associated for me) that has unarguably impacted my job performance over the years. Consequently, despite the fact that essentially every single one of my peers has expressed to me on numerous occasions without prompting that they find my contributions to their own work to be invaluable and that they would not know how to approach solving many of the problems that they encounter without my help, my boss clearly regards me as a charity case. Despite the fact that I have spent a significant fraction of my professional life trying to keep this sinking ship afloat and ultimately bolstering my boss's reputation without adequately advancing my own, and despite the fact that I have (very stupidly but largely as a consequence of my mental health struggles) allowed him to underpay me relative to my peers, it's been clear to me for some time that my boss does not understand the important role that I play within our workplace and does not value my contributions. While I'm genuinely grateful to him for the patience he's shown me as I struggle with my mental health, it's also clear that he's willing to exploit that gratitude by reminding me of what he's done for me while ignoring what I've done for him. While I had hoped that for the purposes of providing a reference, he would see it as being in his own interests to emphasize the positive work I've done for him in order to get someone else to hire me, it seems he's either actually genuinely unable to perceive my positive contributions, or perhaps (the more cynical side of myself thinks) would rather continue to have me beholden to him than find employment elsewhere.
All of that is background and possibly just minimally-relevant venting. My actual question is, given all this, how do I handle this situation as I continue my job search? Time is becoming critical as my contract will expire at the beginning of October, and I am obviously quite eager to escape this situation. This most recent employer was very specific in wanting to get a reference from my current supervisor, and I believe that is going to be standard. In addition to my boss, they spoke with three additional professional references, all three of whom told me they were excited to give me a positive reference, and all three of whom contacted me immediately after they spoke with the company to tell me they'd done so and that they hoped they'd done a good enough job in endorsing me. My contact at the company told me that he'd directly lobbied to the hiring manager that my boss's equivocal endorsement should be discounted, for which I'm obviously incredibly grateful, but clearly that wasn't enough, nor is that an advantage I'm going to have in the future. Is there a way to prepare a hiring manager to expect a not-stellar reference such that they'll understand it may be due to an issue with the boss rather than the employee? (Even worse for me is the fact that my boss is supposedly an expert on "leadership" and has written a book on the topic, a fact that I and many of my peers in our group find darkly amusing, but which I imagine likely makes his assessment seem more valuable.) Unfortunately I have been working for this person for over a decade with only a brief interruption, so I don't have other recent supervisors I can ask to provide a reference to counteract whatever negative or equivocal things my boss might say.
Will hiring managers be willing to look past my boss's opinion? Or am I fucked?