If you are simply copying a paragraph or two (say 150 - 200 words) for an academic monograph, a court is likely to consider it fair use because your use is transformative (for commentary) and your borrowing is minimal. The fact that the work is unpublished weighs against fair use but is not by itself dispositive. (BTW, depositing an unpublished manuscript in a library doesn't amount to publication for copyright purposes.) As for paraphrasing and revealing the plot, we'll get to that, below. But before we digress, we must remind you that a judge may disagree with our opinion -- only a court can determine fair use -- and proving fair use can be an expensive proposition.
Paraphrasing. We don't recommend paraphrasing as a means of absolving you from liability. As one court stated, “We recognize that even in the absence of closely similar language, courts have found copyright infringement on the basis of “recognizable paraphrases.”
Can you reveal the plot? If you agreed not to disclose the plot -- for example, you were required to sign an agreement to access the unpublished work -- then that agreement would determine your rights (especially if it forbade copying). Alternatively, if what you disclosed of the plot was considered the heart of the unpublished manuscript, it may weigh against fair use. Otherwise, we don't see how your discussion of the plot for an academic monograph would amount to infringement, especially if others have disclosed it and the manuscript is available to the public. (The results might differ if you were a fiction writer borrowing the plot.) And, of course, some plots -- boy meets girl, boy loses girl, boy gets girl -- are so stock, that they are considered merely unprotectable "ideas," not original expressions, a theory best expressed in this case.