--with everyone alive.

SPOILERS

You need to swap Yuri's file (or Sayori's) with Monika's. Once they die, Monika always deletes the files. So you could then trick Monika into deleting herself. She'll still be there normal but it's gonna change at the Only Monika ending (beware of jumpscare). Monika will glitch out into a whole bunch of squares and screaming about how much it hurts and why Oliver wasn't helping her. She'll calm down, confess love, then be gone.

OR

You let everything happen, everyone will die until you then reach the Only Monika ending and delete her file immediately when confronting her in that building house. She'll scream, glitch out, confess love, then tell Oliver about how she never really deleted the other girls after they died. Then it will return to the normal home page with everyone alive. The only thing different is that Monika is gone from the title page