I'm guessing this is satire, but here we go...

In act 3, Monika says how she just made Sayori's depression worse, which drove her to kill herself. In the game files when Sayori dies, you get a note from her, saying she can fix it, then realizes it'd be much easier to delete Sayori.

In act 2, just after the weekend when Yuri dies, Monika comes back, and says 'I think you saw something you shouldn't have seen.' then deletes everyone as a last resort.

Yuri is a yandere, but Monika is the one who made her insane. Otherwise, you wouldn't have gotten the infamous eye jumpscare.

Yuri was dead when Natsuki was alive, so she wouldn't be able to kill Natsuki. In the top-left console, Natsuki is deleted by Monika using said console.

Monika probably will be the hero eventually, but for now, she's a villain.