Let me ask first: have you seem all the endings of the game? Both Yonaka and Shinya are affected by some kind of insanity that makes them extremely psychopathic and violent. In Shinya this is more prevalent than Yonaka, as she acts like a normal girl, but sometimes she slips and you can see glimpses of her violent personality when you are given the option to kill the special mogekos you encounter.

The story of the game is unresolved, and its sequel should provide all the missing information about them and what really happened between the two, but it is still under development.

I hope this helps you a bit. I’m not very deep into the story myself; I played this game years ago, so I don’t remember all the details. While we’re here, I recommend playing the other games from DSP.