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.

The fate of Equestria lies in Twilight Sparkle's hooves when two warring clans of ancient, alien robots arrive on the planet in search of a long lost relic.

This story is a sequel to Geoverse Part Five: Prisoner of Love

Twilight Sparkle and Geo have been together for a while now, and they think they've been through everything. But it would seem that, once again, Fate has other ideas. Now everything from evil kings to lords of chaos (as well as everything else in between) will require their attention.

Just another day at the office, then.

AUTHOR'S NOTES

Part Six of the Geoverse.

Rated Teen for bad language, violence and suggestive sexual elements.

Each chapter will be set during or after a Season Three episode, with our three human protagonists thrown in.

Once again, the wonderful Crimson Star is my co-author.

All Bonus Chapters are canon except for the first one, and any with (NC) in the title.

Hi and welcome to the story "Bobobo-bo bo-bobo: The Land of Colorful Ponies". If you look to your left, you can see that Bobobo and the gang went to find something to do on their day off. If you look to your right, you'll find Twilight and the girls having a wonderful picnic in Ponyville park. And if you look at me, YOU'LL FIND THAT I'M AN ORANGE STAR INFRONT OF YOUR FACE!! HAAHAHAHAHA.

You were expecting a different cover art weren't ya? WELL TOO BAD!!

A magical portal leaves Fluttershy stuck in a strange place with no way home. What are these loud, frightening creatures she finds and why do they turn into cute little animals when you bump into them?

A crossover with "Fruits Basket".
Written with help from SirFrancisBacon.
Edited by Peregrine Caged.

*Please read whole thing before beginning story*
After having the same nightmare for the past three months, Twilight goes to Princess Celestia for help. But after Princess Celestia tells Twilight that the nightmares are memories and not dreams, Twilight must make sense that her soul is eternal and has been living for the past thousands of years. With the return of the Crystal Empire, Twilight must reawaken the other Sailor Scouts, in their present-day pony forms, and they must set out to vanquish the evil that comes along with the Empire.

--I know there are a lot of Sailor Senshi and various different villains, but this is my take on it with a pony spin. Not all of the Senshi can or will be accounted for, so please don't just dislike the story because your favorite Senshi character isn't included. And please don't just negatively rate it because I'm using the Senshi's English names rather than their Japanese. I respect both names, but I grew up with the English anime and that's what's most nostalgic for me.
Just a crossover I wanted to try after reading this article http://sailormoonnews.com/2012/11/12/is-my-little-ponys-crystal-empire-inspired-by-sailor-moons-crystal-tokyo/#more-1059 --

One would think that the wounded Trixie would appreciate Twilight Sparkle taking her in to nurse her back to health. But for some ponies, leaning on someone else isn't so easy. Their crossing of paths sets them both on a journey that neither of them would've expected...

They take… really long bubble baths.

An indirect sequel to “My Little Staring Contest: Alicorns can stare for a very long time.”

Part of the All-American Girl continuity.
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For Derpy Hooves, life is never easy. Even as an accomplished scientist and scholar, she still has to contend with a twin sister that hates her, living alone in a tiny town and working a dead-end job, and, of course, her eyes, which causes her to be clumsier in public than she normally is. For her, life sucks.

But now, Derpy has to face a decision that could rock the very foundations of her family, her life and her future. And if that wasn't enough, one of the neighborhood foals, Sparkler, may need her help desperately. And to top it all off, a secret project of hers might just change the world of ponydom forever.

She's got a lot on her hooves. Maybe too much.

After being rejected by Rarity, Spike falls into a state of depression. There he becomes friends with an unlikely pony, Diamond Tiara. As they become better friends, Spike finds himself drawn to Diamond Tiara in more sinister ways.

Spike x Diamond Tiara ship. No foalcon.
Officially approved by the Diamond Cutters!