HOW Miyuki kills Shinichi...we don't see it, thankfully, but we can hear it, and the mental picture is not pleasant.
The entire screen being drenched in blood and fading to black while Miyuki's "Happy Birthday" gets cut short, the game "reboots", and she takes over the game. If you haven't played a game that's done this before (e.g. Doki Doki Literature Club!), it can be quite unsettling at first.
The changes that Miyuki makes to the rebooted world ensure that every attempt the player makes to escape and find Aoi are futile. You can't save or load the game, Miyuki drugs Shinichi so he is incoherent and the player can't influence him to resist her, and even when you do find ways of progressing the story, Miyuki sets things up so that you don't get very far.
Miyuki: Why? Why, you ask? Because YOU won't love me! Why won't YOU return my affection? I love YOU so much! So much I have to kill YOU! I have to kill the person I love, over and over and over again! I'm losing my fucking mind!
The other infamous scene: once you butter Miyuki up enough, she will get Shinichi to say he loves her a hundred times, only to knock him out with her bat. Turns out what she really wants is for the player to confirm their love for her, the only way she can think of- sex. Cue a ten minute, unskippable CG of Miyuki masturbating on top of Shinichi's unconscious body, getting more unhinged and crazed until she climaxes.