Towards the very end, everything flips around and the deuteragonist turns on protagonist, forcing him to join up with the "good guys" to stop the now-antagonist, but this is so late in the story that I don't feel right calling them "supporting characters" or the deuteragonist the "antagonist", so what should I call all these characters?
Most Helpful Girl
The antagonist is usually used to refer to the villain, but it doesn't always have to. It's just the person opposing the protagonist.
As for what happens towards the end, I'm not sure what you'd call them. I guess the antagonist changes towards the end, or you could have a primary and secondary antagonist.
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Most Helpful Guy
Your protagonist is your main character while the antagonist is the one opposing them. These particular terms shouldn't be in your story though.
That's all those words actually mean, your two main characters, not Neccessarily the good guy and the bad guy.