Idea 1: If it was in the events of the actual games
Basically, there would be no 4th wall breaking or meta storytelling, it would be the actual Sonic characters fighting for their lives against a Sonic being controlled by his own negative chaos energy.
Basically the same plot as the original part 1 and 2 but tweaked MASSIVELY to be more... not make you cringe every paragraph-y. And some original things too.
I've seen a lot of people recreate the sonic.exe story with fangames, And they're pretty good (even tho being better than the original is a low bar) so I wish you luck