What's a Yume Nikki fangame without mounds of WMG and headcanon in attempt to explain the abundant Surreal Horror weirdness? As with the main page, beware many unmarked spoilers ahead!
In this headcanon, the protagonist's mother was killed when they were very young. In their despair and desperation, they had fled from the sewers. The reason could be anything from “there are hostile alien/hybrids who would gladly take advantage of an orphaned hybrid” to “they just wouldn’t be able to survive on their own in the sewers”. So, they stayed on the surface, possibly in order to be able to more easily obtain food by attempting to pose as a normal human street rat.
Here’s where the woman comes in. She had found the little hybrid still in mourning and took them in. She was lonely and the child was orphaned, and with her riches she was certainly able to support the child. She would raise them as a human, pulling them from the oppression of being a hybrid, though she never let them forget their heritage. She taught them about Christianity and took them to church with her regularly. She also liked to take them to the theatre (where they’d joke that one day the little alien could be a performer too). All in all, she liked to get the child out into the world as much as possible. More than anything, she protected them and took care of them, shielding them from oppression and most of all hiding them from the eyes of Terra Puritatem.
In turn, the protagonist provided companionship and just something for the old woman to live for. As they grew, the old lady grew more frail and sickly with age. The protagonist grew worried for her, since they were around for her less and less (most likely training to board the shuttle that would take them off to the Harmony). However, they didn’t want their adoptive mother to grow lonely again. So they began to work on something for her: a doll. A little doll made of patchwork that she could hold on to once they were gone.
But before the protagonist could finish the gift, a few days before they were ready to board, the old lady died. And in the protagonist's mind, she died just as lonely as she was when they had met her. That’s why you must collect the doll parts for the first half of the game. The protagonist felt guilty for never finishing the old lady's gift; this is why you must first give her a friend before traversing the darker part of the game: you have to defeat the protagonist's most “recent” darkest memory before getting to the horrific repressed memories underneath.
Source of this WMG is this Tumblr post.
Source of this WMG is this Tumblr post.