Hey dude, just though of an sonic.exe type of story on touhou.
So basically, you play an completely normal touhou 7, everything seems normal all things considered with all the bullet hell, still hard but it's touhou. Until once you bet flandre, the secret boss (I think flandre is a secret boss or the final boss. Correct me for this). You'll think you'll finally beat touhou but you'll get to meet someone new. Now, if you know touhou enough or your a big fan (or a "fake" fan that only knows touhou in medias like me and didn't actually play the damn game), you would like see this curiously, shocked, or you thought that this is in the game and you probably forgot (or your new). Once you finished this "final" boss, which is actually very easy compared to everything. Which is strange, almost like it playing with you. And then there would be two choices that would appear for you to move reimu to, deny or accept, tell for you (the player) to join with it in the game (ohh~ this is where is gonna be spoopy~). If you accept, it'll reach out a hand for you to take. Either or not you also reach for it, you'll be knocked out (not like somebody hit you at the back of the head or something :/).
And then Boom! You're in the the game :)
And you thought that you would be the only sentients there, well, everything there to people, youkai, and the other major characters (and others that are not even on the game yet) are fully sentient. Like you have actually been pulled from reality and to gensokyou (like yukari does with different fanfictions with different y/ns or ocs).
But, you be stuck as a character of whatever the entity chooses what character you'll be in. You can either be as reimu, Marisa, even yukari if it wants it to. but you'll be likely put in a random youkai or fairy.
So, summery. Normal touhou game until you get trapped in the game. Nothing really scary about that huh.
But, you can decide if you want that entity to be malicious or not. See what you think :)