Hmm... That's weird... Anyways, for my hack, I had an idea, that at some point Team Magma and Aqua are arguing and using the random XSE command, you will get
a)kidnapped by Team Magma leader
or
b)kidnapped by Team Aqua leader
You get brainwashed by them, and for a beta (2 badges) the story changes drastically because of that, until the player snaps out of it :D
Good or no?