So as I was framing the most recent SAGE story (!) I happened to think "What if someone asks me who the villain or antagonist is?" Well, by that I mean I know no one would ever ask but this is the sort of thing I think about.
One possible answer is, there isn't a physical one. SAGE's mental health provides enough of an obstacle. I can only recommend that you remember just how unreliable a narrator SAGE is. At any given time she can only remember about 60% of her life with varying degrees of relevance (i.e. knowing she likes cornflakes, but not how many children she has) and 0% of her love life. That being said, what you learn about her past has been filtered first through her perception then her psychosis, so the final written version in her journal (which despite then tone she {IC} never expected to be published) should be taken with enough salt to choke a horse.
Having the ability of author foreknowledge, I can say that in my own interpretation SAGE-sama falls more along the lines of chaotic neutral at best anyway (rendering a villain sort of superfluous). There have been hints of some of her more serious, and lasting, misdeeds but you'd have to have been really paying attention to catch it. Then to extrapolate you'd need to be John von Neumann or something. In the end your mileage may vary; this is only my opinion remember. We will get to see some evidence of that facet of her personality in the future though, so buckle down.
Oh yeah. K-On! ended. Without yuri. *sigh* Oh well.
The D&D online alignment quiz says chaotic evil, but that seems a bit harsh