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.

The TV Tropes page can be found here.

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.

Spin-off story to "Sonic Generations: Friendship is Timeless", taking place between chapters fifteen and sixteen during the train ride to Canterlot.

Everyone knows that Sonic, Tails, Spike, the Main Six, Shining Armor, and Princess Cadance set out for and arrived at Canterlot aboard the Friendship Express to find and stop the monster that had intertwined two worlds and their fates together, but what happened along the way? While Princess Celestia and Princess Luna went on ahead and prepared for their arrival, Equestria and Earth's heroes had to go through more adventures in order to get to Equestria's capital city. Now, the story of their lesser known adventures shall be told.

So climb aboard the Friendship Express, grab a seat, and get comfortable. It's going to be quite a ride.

Sonic Generations: Friendship is Timeless TV Tropes page can be found here.

While foiling one of Robotnik (Eggman's) plans of world conquests, Sonic is unknowingly sent to Equestria and meets its heroes But he doesn't come alone; something else has followed him to the land of ponies. A power that could destroy the very land beneath his feet.

In the struggle to win the war and restore peace to Equestria corrupted ponies turn on the royal sisters and harmony itself. In an attempt to defeat the "corrupted" The Princesses allow the heads of science and development to design a cure for the corruption that takes more of Equestria's population every day. But the cure is alive and has its own ideas

"Discovering the secret of my past will be nearly impossible ... I'll take those odds."
~Shadow The Hedgehog - Video Game Trailer

(based off of SEGA's Shadow The Hedgehog).