How do you continue the desperate girl storyline, after helping her?
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Glad to hear it. I tried to replicate it too but I wasn't successful.
The closed apartments doors are my "clever" way of managing random procedural generation with a still limited pool of rooms (more will be added later). Basically, the more you progress in the game, the less chance there's to have a closed room. It's a way to limit the number of available room at the start of the game so you don't immediately see all the rooms. You can see it as a representation of the rooms you've yet to see.
Thought I'd report a bug I've encountered: (I presume this is the cause, since I can consistently reproduce it, after finishing the Hospital/University - up to Brookside Glade) If you attempt to enter an apartment with this room unlocked (one of the ones that said "Restricted. Keep Out."), your game crashes.