Grad school admission after bad grade in research class for different discipline I have a predicament. I am about 4 weeks shy of graduating from a small Virginia (USA) school with a BA in English literature and I received a D in an upper-level research class in linguistics, which I do not intend to study in the future. I want to apply to a graduate program for English lit in the future, and I am otherwise qualified (otherwise great grades/GPA, great test scores and letters of recommendation, four conference presentations, and a highly prestigious award for an undergraduate research paper in literature). I am very nervous that this class will kill my chances of getting into a good masters/PhD program. I plan to explain that the class was in linguistics, which was very far out of my comfort zone and I had very little prior knowledge of the subject or research methods required to succeed in this class. I felt like my professor expected more from me than I was capable of because I won awards for my research in literature, and she assured me that I would be qualified to perform this research without realizing that my research had been exclusively literary until that point and that I would need extra help to succeed (which she was never willing to provide despite me practically begging for help). Do you think this situation would kill my chances of getting into a good school? Or do you think they would be willing to overlook the abnormal grade since it was not part of my area of study? 

It might also be important to note that I failed a literature class and retook it and earned a B+. The "F" is still visible on my transcript but doesn't factor into my GPA. I received the grade because I could not turn in my final paper due to a one-time extenuating circumstance, but my performance was excellent in that course until that point. 

This is a super long and complicated question, but I'm taking a gap year to figure myself out and gain professional experience, so I'm not looking at any urgent upcoming deadlines. I just don't want to set myself up for failure by applying to schools that wouldn't give me a chance. I'm more than willing to go into an MA program at a smaller school to work hard and prove myself to a big shot university. I just don't really know what to do and professors at my school are not being up front with me about my situation because they don't have the full story. Everyone I work with says I have a great chance, but I am having doubts.
Welcome! The gap year is a good idea. A lot of research in graduate school (and beyond) is (in my experience) similar to that linguistics class: confusing, unstructured, little guidance, figuring methods and new things out on your own, shaping your own experience. So the best way to set yourself up for success is to figure out what you could do differently in a similar situation to succeed. Where else could you find resources? How could you figure out direct questions your professor could answer? (Or that a different professor could answer for you?)

There are similar questions about recovering from a bad grade, such as this one: How does the admissions process work for Ph.D. programs in the US, particularly for weak or borderline students? and this one: Does a bad grade in one course (with otherwise OK record) affect graduate admissions?  

You may or may not need to explain what went wrong in that linguistics class as part of the graduate admissions process. But you should get it straight in your mind so that you have clearly learned from it, and so that you can deal with this better when you encounter similar situations in the future. That is, you can take charge of this story and it becomes less about that professor and more about a mistake or a problem that you've learned from and figured out how to overcome.  Good luck!