What if Eggman hid in Gensokyo and Sonic had to go find him?
Sonic would have to go through the Shrine Zone, Magic Forest Zone, Human Village Zone, Bamboo Labyrinth Zone, Frozen Lake Zone, Scarlet Basement Zone, Sunflower Field Zone, Youkai Mountain Zone, Underground Reactor Zone, and finally the "Totally Not Eggman's Secret Lair" - Zone to find him.
As he progresses through those zones, he must battle with a touhou character that serves as each zone's "boss."
The chaos emeralds are found in Yukari's Gaps (special stages) for whatever reason...
Should Sonic collect all the emeralds, he must go Super Sonic to fight against a
Magic-Enhanced-Eggman-Death-Machine-Who-Wields-a-Crescent-Staff-That-May-or-May-Not-Have-Been-Stolen-From-Mima-That-Shoots-DanmakuTM, which would be the true final boss.
What if we got a
Strange-Matter Youkai? (It can either be one that literally is a Strange Matter youkai, or one that can manipulate it)