Oh, that's good to hear. I'm looking forward to what you come up with next. To help get you into the mindset of what it would be like to have a paranoid version of the Doctor, consider this:
First, start with the Doctor. The Doctor gets a Final Destination-style vision from his perspective, which contains the events up to and including The Woman ending. After returning to the start of this game, the Doctor is spooked at first, but after seeing enough events that match the "original timeline", he becomes nearly convinced that Yumeko is an imminent threat.
Which could end up with something like this:
_
Doc: "I know you're up to no good, Yumeko. I know the horrible things you're planning. So just confess, okay? I won't be mad, just spit it out."
夢子: "Confess? Confess what?"
One of the voices: You've never seen the Doctor like this. He tends to be agreeable if you don't anger him, but something seems to have bothered him last night. A bad dream, perhaps? Or something else?
Doc: "Oh, I see. You want to play dumb. You want me dead, Yumeko. We both know this. So be honest, and admit it, will you?"
One of the voices: While you wouldn't be too upset over the Doctor's passing, it is unlikely you would be able to last long in his laptop on your own.
Another voice: However, that isn't important right now. If you say what he wants to hear, you'll be immediately shut down. But if you deny it, he'll shut you down for lying to him. And he looks very angry right now, so staying quiet won't get you anywhere.
> Yes, I want you dead.
> No, I would never want that.
> ...
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After Yumeko is shut down, the Doc brings her back a month or so later, having changed his mind. However, he has installed some additional safeguards that he thinks are necessary to his safety. The rest of the game is about managing the Doctor's paranoia, ultimately leading to Yumeko's escape or destruction.