The Brain Icon
Quite simply, it's not Fran. It's not what she's become, or anything. It's her THOUGHTS. There seems to be different icons for Mr. Midnight talking or thinking, as well as Fran talking or thinking.- I've seen a theory that's based off of the doctor saying to extract the brain that claims that the entire story is Fran's recollections after being brain-in-a-tanked.
Itward is an angel
Specifically Fran’s guardian angel, an especially powerful one given Remor is afraid of him. Also, at the end of the game he takes Fran to Heaven. Little Fran
In that section where Fran meets a younger version of herself, little Fran says that she doesn't have a cat. So this version of Fran never had the freedom to get the cat, seeing as she's seen in an asylum ward, which implies that her mother never ran away to hide her from Dr. Oswald (his picture is even on the back wall). Is little Fran destined to be experimented on for whatever special power her brain holds?