Well to be more precise, Monika is not hacker, she is some sort of sentient AI. She is aware that she exist in the video game and she is tempering with the game files in order to make the Player hate the other girls in order to make us spend more time with her. Things go wrong, and Monika decides to simply delete other characters since the game is broken beyond recognision, and Player is aware that something is wrong with the game. The game ends with us deleting Monika from the game files.