Dear Mariko

Yes it does. The introduction says "'Mariko' / The way he said my name..."

And then the way Mariko acts is suspect. Supposedly Mariko knocks on the front door of her own house before entering - I don't know anyone who does that. And then she walks in openly brandishing a knife - which is illegal in most places I know of. When she reads the letter, she says "I'll kill you." And (if you hide in the bathroom) she breaks down the door. And then she actually murders you. Either Mariko herself is criminally insane, and Darien has a thing for yanderes, or this plot makes no sense.

It just feels like you made the game with the intention of the main character being Mariko, and then at the very end, when you were writing the true ending, you decided that the other girl should be Mariko instead.

Here's what I can buy:
-We hear Mariko before she enters the house. (makes sense)
-Mariko knocks on her own door (as long as it's explicit that she's hoping Darien will open it). I could buy it easier and better if instead of hearing Mariko knocking, we just her walking up the front steps.
-Mariko has a knife (since the protagonist can't see her, it could just be her imagination).
-Mariko says "I found you!" and the game ends (because the game is up - no pun intended).

Here's what I can't buy:
-The introduction being told from Mariko's point of view. It's confusing if you don't know the protagonist isn't Mariko, and it's pointless if you do know it. Removing the references to Mariko would fix that.
-Mariko says "I'll kill you." What the heck?! Just remove that.
-Mariko breaks down the bathroom door. WHAT?! I didn't even believe that when I thought she was the crazy girl. No one is breaking down a door with a knife. It should just be that she's still there when you want to leave, and there's no other exit besides the door.
-The screen flashes red if Mariko catches you, and it sounds like you're getting stabbed. The real Mariko shouldn't be a violent murderer like this game makes her out to be. Just remove it.

Yeah, there are a bunch of hints about the true ending, and I realized them after I found it (I went back and played it again from the start). It doesn't change my comments one bit. Even knowing you had the plot planned out the whole time, it still felt like you did the ending last and went back and added those in afterwards, because everything else is so confusing as it stands.

I can tell you're not open to changes because you're defending your decisions. But I'm just making suggestions because I care, because I actually liked something about the game, and want to make it better. To that end:
-The part of the introduction with "I met Darien 2 years ago" could be Shinku as easily as Mariko. Same with the part about something being wrong with Darien, because Shinku obviously is not getting that Darien doesn't want to be with her.
-As I understand it, the idea that "Mariko has been endlessly harassed and threatened" is impossible because until she read the letter, she had no idea that Darien had a previous girlfriend, or that he was being stalked. The intro makes it clear that she only knows "something is wrong between Darien and me." That's not enough for someone to feel a need to arm herself, or be determined to find out who Darien's stalker is. Basically, it seems like you wrote Mariko's lines as though she had no knowledge of a stalker (but the way she reacted to that letter was pretty stalker-ish herself), but wrote Mariko's actions as though she is being chased by a monster at this very moment, and it doesn't mesh together. That's why I suggested the changes I did.

I don't quite get why the first thought of any loss or bad event happening is to "get back at her", grabbing a knife and being out to kill someone. I know it's an animu thing to do, and happening a lot in horror .. still seems so odd.