I am in the progress of writing a novel that I intend in the end to become a great tragedy, wherein there ends up being no real villain (hence the tragedy). I am wondering as to thoughts of what and what not to do with such scenarios, in order to make it as intriguing as possible? From the start through more than 3/4 of the way through the face of "villain" changes a few times, as plot twists play out or backstory is revealed that sheds new light on certain situations.
The thing that sticks out to me about your execution is the phrase " plot twists." Be careful, plot twists can be amazing, where you have the put the book down and let your brain absorb what just happen, but in a lot of modern fiction such twists are predictable. So my only piece of advice in doing something like this is be careful with twists. Don't use anything too cliche, but don't do anything too far out of the blew where the reader feels cheated by a deus ex machina.
Read the book "The harafish" but skip the last chapter. You then have a villain-less tragic tale. It will allow you to see one way that such a story can work out (damn good read too)
There are different ways to approach tragedy. The ancient Greeks construed tragedy as the consequences of trying to escape one's destiny in defiance of the gods. For an example, look at Medea. Shakespeare often centered tragedy around accidents of timing (e.g. Romeo and Juliet). The more modern view of tragedy often arises from personal flaws and weaknesses (Death of a Salesman). Consider using any of these, or a combination of them, in your story, although accidents of timing are more often central to comedy these days.
Tragedies aren't villainless. Their defining feature is the tragic fall, whereby the tragic hero, who begins in a 'high' place (respected, noble, virtuous), falls due to their tragic flaw (hubris, jealousy, impiety). At the end, they realise the error of their ways, but not in time to save themselves or the other victims of the tragedy, and in most tragedies from Shakespeare on (and many of the ancient ones), the tragic hero dies. That arc is what defines a (literary) tragedy, nothing else.
I interpret this to mean that your story has several "villainous" protagonists or characters, so that in the end the reader can't say "John was the good guy, and George was the bad guy, and Marianne was the traitor who seemed good but was actually allied with a third group of bad guys." The book Tigana did something similar rather well -- the main "villain" was quite sympathetic, and the good guys frequently did things that resulted in people dying or, in one case, being essentially enslaved. Although the ending turned out reasonably cheerfully under the circumstances. So, my advice is fourfold. First, make several interesting characters, one or two of whom are mostly good. They don't have to be shining-bright-happy good, just well-intentioned, intelligent, or competent, or posessing other characteristics that make them generally good. This doen't mean that they have always been good -- you can play around with this, having a character who, say, was a rapist or a murderer when they were in their late teens, and who, after years trying to make up for it, is now a "good" person who has done terrible things. Second, make even your villains admirable in some way. The bad guy can be misunderstood, or a good leader, or a loving father or a caring mother or motivated to do whatever he's doing by a cause many of us would have sympathy with. Or perhaps one of the main characters is telling the narrating (point-of-view) character about the bad guy, and lying about it or exaggerating -- so you spend half the book thinking the bad guy is a complete monster, but it turns out the character's companion was lying and the bad guy is actually pretty okay. Third, make your character do something terrible for what they think is a good reason. The university and all of its folk will be overrun unless you flood the river to block the encroaching army, a move which will kill anyone downstream, including many innocents. The bad guy's sister is trying to warn him so the main character kills the sister. Assassination. Deliberatelay being cruel to a person so you can distract them and stop them from accurately weaving their spells. Fourth, have the good guys lose something they would care about. If there is a single very good person, he should not be completely victorious. Perhaps he never finds out what happened to his family. Perhaps he has to do something terrible (see above) and never really quite convinces himself that it was okay to kill those people in order to save his family. Perhaps his family is angry -- or some of them, anyway -- that he had to behave so barbarically. Perhaps the bad guys win most of what they wanted, and the hero, now disgraced or fallen, has to make his own way in a now strange and hostile world -- not having lost everything, but no longer having a country of his own.