I've seen this idea done before, but as a fan of Sonic and MLP: FiM, I wanted to give it a go myself.
This, basically, is the story of Sonic Generations, but crossed over with the MLP:FiM universe, with Spike and the Main Six taking the place of Classic Sonic and Classic Tails with other MLP characters also appearing (most aren't listed to prevent spoilers). Except for Green Hill, there will be different areas explored, as well as pony rivals and different era bosses. So while it will have its similarities to the console and 3DS versions of the actual game, it will definitely have its differences too.
Also, in case anyone was wondering, there will NOT be any shipping in this story. At the very least, no crossover shippings. No SonicxRD, TailsxTwilight, TailsxFluttershy, or anything like that. If there is any shipping at all, it will only be between characters from the same universe. And the only humans in this story are Dr. Eggman and the ones that appear in the "Sonic Unleashed" level.
A big thanks goes to bvge on Deviantart for creating the new logo on the cover art. It's a vast improvement over the old cover art.
NOTE: Due to the length of many of the chapters in this story, most of them have been broken up into smaller parts of roughly 10,000 words or less to make the story easier to read.