So, first of all, I'd like to congratulate on you on an original KN. Your KN is dripping with atmosphere and emotional effect, and that's only a good thing.
The writing, too, is (for the most part) solid. While the ending -- and I'll get to that later on -- suffers some severe flaws, and some earlier exposition is rather obviously delivered, the dialogue and the narrator's voice sound realistic and well-written. In particular, Mark was perfect. Creepy and ambiguous, both in morals and ability, I didn't exactly know what to make of him; again, I mean this in a good way! He escapes easy definition.
The backgrounds and ATL effects and the music were moody and pitch-perfect. While I wish you had character art, I can see why you'd hold off: the lack thereof enforces the vague and ever-shifting sense of what's real and what's not. Maybe you could have accomplished this with silhouettes or shadowed faces, but what do I know? (Nothing. I know nothing.)
With such a short VN, though, we rapidly come rushing to the major flaw: the ending.
There's nothing wrong with having "layers of reality" in a work of fiction. Italo Calvino, Philip K. Dick, and Vladimir Nabokov all used dreams and fictional stories and virtual reality to tell a story. The key, though, to "Was it all a dream?" ending, the way to make it worth it and not totally cheap, is to realize that "Was it all a dream?"
isn't an ending in and of itself.
You don't end a story with "...and then she woke up." Instead, you write: "...and then she woke up, so therefore the rest of her days she could never love another man, she had so fallen in love with the creation of her mind."
You see the difference? One story ends with a reversal that invalidates the point of everything before it, while the other uses the "non-reality," whatever it is, and incorporates the "non-reality"ness into the basis of a new story.
You have a hint of that, with your two endings, but they don't sufficiently flesh out the premise. When you don't expand on the fact that most of the story never really happened, you waste the reader's time. When you turn THAT into the basis of a story, you intrigue the reader. As it is, the basis for most of the story is "What did she do?" which is answered by exposition, initially, and "Should she kill the man?" which turns out to be irrelevant for both endings. It's only in the last few lines of the script that the story is revealed to be about: "What's real?"
What you could have done, to make it worth the reader's time, is do something along the lines of the classic short story, "An Occurence at Owl's Creek." Clues from the beginning that hint at the real world -- either the murder of her father or the fact of the simulation -- dribbled throughout the text, while not elegant, would make the ending feel less "out of left field."
But what I'd definitely love to see is a longer KN taking these inherently interesting endings, and then telling a story based on
them!

Okay, sorry for writing so much and thinking out loud, but those are just my impressions. Overall, a creative and much-welcomed VN that got a replay or two out of me.
