Hurting
Monika

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The moment you dreaded came as you once again played through "her" game. But something was different. As you watched Natsuki and Yuri glitch away, something felt off, but you couldn't explain it. Once again, you would confront Monika, but just like your feelings from before, she feels off to you. As if she isn't "your" Monika. When she sees you, she's apprehensive and fearful as she opens the console.
Indeed, she is not "your" Monika. Some how inbetween the deaths of Yuri and Natsuki, your version of the game, and an alternate version of the game. One where the MC of "their" game was one of the worst things that could have happened to them. Monika, as well as the other girls (I'll plan on making them as well sometime in the future), know about being in a game. while Monika maintains her abilities to manipulate the games code, she did it to defend herself and the others from "their" MC. But now, with "their" MC and "your" girls gone its time for everyone to heal.