(Note: I haven't finished Samantha's story yet, so apologies if that somehow renders my suggestion pointless.)
Hmm... Let's see here... One thing I was initially disappointed by was the fact that the closest thing to "slave" content in the game so far was of the rape/abuse/punishment variety. I've always preferred the more happy and willing type of slave, especially in mind control games. And, as someone else mentioned, the protagonist does tend to try to take an oddly roundabout way of brainwashing these girls, using the mind control to create excuses for non-MC porn scenarios rather than bending the girls to his will.
BUT it's clear that you want the game to go in a particular direction that doesn't necessarily gel with what I was hoping for. A particularly goofy direction, at that. So how about we combine the two, and twist what I was hoping for into something goofy and off the rails? Have the professor attempt to directly turn her into his obedient slave, perhaps by offering her a job as his assistant and slowly turning her respect for him into worship... But then things go off the rails as she gives in to the brainwashing too easily and starts taking a more eager and proactive role in serving him than what he originally planned. When she discovers that he's been hypnotizing her, she becomes even more eager to serve him. It turns out she actually has a fantasy about being a minion to an evil genius! She becomes the Igor to his Frankenstein, the Renfield to his Dracula, and the Pinky to his Brain. But her ideas about what makes a good minion take priority over the Professor's attempts to turn her into an obedient sex slave, so he spends most of the storyline trying to satisfy her minion fantasy instead of using her for his own pleasure. She gets upset when he concocts evil plans without her, so the later parts of her story have him using her to help brainwash other girls, with varying degrees of success as things go hilariously wrong or hilariously right.
There could be a scene where she hunches over like Igor and says, "Yessssss Massssterrrrrr," and the Professor would be like, "What the fuck are you doing? Stand up straight, and speak clearly!" Maybe throw in some eager/Igor puns, too. "I hypnotized you to become my EAGER slave, not my-- *Sigh* Never mind..."
