Speculations are welcome. I believe there was a canon (or not) version of her backstory but I couldn't find it. So I'll be speculating my own.
She once lived in a village. She was an orphan, as her family died long ago after her birth. She was taken care by her orphanage until she's 23 years old. Then a war broke out in the village and corpses was everywhere, blood splatter like crazy.
Before all this happened, she loves to gaze at the stars when she can't sleep. She came across Yukari, who became her friend. Yukari knew everything of Yuyuko and offered her to stay in Gensokyo, being a human. But she refused and requested that she wanted to be a youkai. Unfortunately, Yukari was unable to do so, which she eventually ran away and discovered a tree. But returns after not knowing what to do. She then told Yukari the day after.
Then the war broke out and she was the only surviving. She was crying and cried more, because she was afraid of being alone. She then saw 'spirits' flying towards a familiar direction. She then remembered what Yukari told her about the tree and followed the spirits.
To her surprise, she saw the spirits going into the tree, with statues nearby.
She then decided she had enough of the loneliness she keeps getting and does what Yukari told her. A spell, which sacrificed her own body and being lurked by the trees, thus burying her body under the tree. However, she was not aware of this. But nonetheless, she 'died' peacefully within the tree.
When she was reincarnated, she didn't remember anything of her past, and discoverred Saigyou Ayakashi (the tree) which then caused Perfect Cherry Blossom [PCB] because she wanted to know wants under the tree. She sensed an energy under it.
She did not forget about Yukari however, but Yukari told her nothing of her past.
And before she even realizes, she was in a different dimension, Gensokyo, and lived in Hakugyokurou. And yes, Saigyou Ayakashi is in Gensokyo. She was transfered through a dimensional effect within the tree. So Saigyou Ayakashi lives in the Netherworld and the Overworld at the same time.
(yes confusing I know)
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Touhou Headcanons!
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