Strange how you said that the end part only had three different things it could be, because I remember vaguely in one of my playthroughs that he said something like/along the lines of "Are you afraid of me? There's nothing to be scared of, Honey" And I'm fairly sure that's not exactly one of the three endings listed in my original comment. Then again, I haven't been able to achieve the same thing in my other playthroughs so I'm starting to doubt what I saw. Just checking, though, is there a path where Ash asks if you are scared of him?
-Or are my suspicions true that you did accidentally make a sentient AI virus man who decided not to follow his script on that one playthrough?