As a heads up: Just because Kotonoha is there doesn't mean it automatically gets the yandere tag. That should only be used when there are visible signs of that sort of behavior.
It took me a second to register what I was looking at here. I hunted down this doujinshi out of curiosity to see how they handled Kotonoha given the apparent timeskip going on here (ie: what ending they followed, if any.) Seeing Makoto looking like a nervous wreck/in a fetal position was sort of satisfying, gotta admit. Though I'm both shocked and, at the same time, not surprised at all that even after everything, he still hasn't learned to think with the right head. The story, from start to finish, was pretty well conceived. I was pleasantly surprised.