Dead.

It all happened so fast. One minute they were there, and the next she was standing in their ashes.

Lost forever.

It wasn't fair. They’d devoted their entire lives to defending Equestria, and what was their reward? To be cut down in the blink of an eye. Weren't they supposed to be the heroes? Weren't they the good guys, the chosen ones, the saviors of the land? This wasn’t the way things were supposed to go!

Alone.

Twilight wouldn't accept it. No, she couldn't accept it. How could fate be so cruel? Why did she have to be the only one left alive? Why did she have to suffer on with such a terrible burden, reliving that terrible moment again and again for all eternity? No, regardless of what anyone said or did, she knew that a terrible mistake had been made, and she would see it fixed...

...no matter what the cost.

MLP/Shadow of the Colossus crossover.

Picture by Companda.

Arceus has been imprisoned for many millennia, and in that time he has watched his world fall apart. But once he is finally freed from his prison he decides that to protect his Pokémon, and his family, that he will move the Pokémon, and a few select 'humans' to a world where they might live in peace, Equestria. However, not everyone on this new world shares his view of peace and the very presence of the Pokémon upsests some of the citizens of the world, even some of the ones he brought with aren't too happy with the situation. But a god's will is a strong thing and without his willingness the Pokémon and the citizens of Equestria are going to have to learn to get along, or at least tolerate each other. And there's a slight problem with some of the humans too, well, former humans that is.

Big thanks to tdnpony for proof reading, editing, helping me with ideas, and so much more.

Just a few of the side stories from my growing collection.
Pokemon, A Whole 'New' Frontier
A New World, A New Way-Swarm.
The City is Always Bustling On the Other Side
A Brave New World
A new World, Burning an Old Way

The rest can be found here, in my Fan Group. Group Linky.

Big thanks toxBUBBA1995x for the amazing new cover art!

I also have a Tvtrope page that is kept somewhat up to date by Kingofsouls if you know how to Trope, and want to help set it up, go here Tvtrope Link.

Since a lot of people keep aking this I'm gonna put an explanation here. I'm not following any one canon-verse here, I'm making a hodge podge universe with bits from the Manga, Anime, Games, and Movies, as well as some etcetera concerning issues addressed in none of them to great lengths. (Arceus' power is far beyond what he has in the games or movie and this does contain some Pokephilia, which comes from pretty much no canon material ever.)

Life has been mostly the same for the girls ever since they had to give up their Elements to the Tree of Harmony. Of course, this couldn't possibly last too long, and strange things begin to happen to our intrepid heroes.

Let it never be said that you can't have too much of a good thing.

Take place after Twilight get her element and before Lightspeed Rescue.

After hearing about where the new Element Ranger came from. Scootaloo, Apple Bloom and Sweetie Belle goes in and come out as a new team of Pony Rangers. Jungle Beast! Spirit Unleashed!

Scootaloo as Jungle Fury Red
Apple Bloom as Jungle Fury Blue
Sweetie Belle as Jungle Fury Yellow
Much later, Shining Armor as Violet Wolf Ranger
Much, MUCH later, Babs Seed as White Rhino Ranger

The animal spirits from the show are in here to give them their powers. The Cutie Mark Crusaders first time as Pony Rangers. Shining Armor is added to be the master of the three once he discovers the rangers. Babs Seed join on a visit.

EDIT: The past chapters of this story were deleted 11/8/2014. If you wish to read them, PM me and I will send them to you.
The Everfree Forest. You've heard the stories. Ponies that go in...never come out.
Shadowflash, abandoned as a filly, has grown up with wolves her entire life. Well, as long as she can remember. Now, the forces of nature destroy what little faith in the forest Shadowflash has, and she is determined to save her pack. In order to, she travels to Ponyville, the one place she never thought she would see again.
As she gets accustomed to pony life, the dark secrets of her abandoning haunt her dreams, and familiar faces start to show up everywhere. And then she is pressed to make the decision of her life:
Pack Life?
Or Pony Life?

Liz is a smart girl. She knows what she's doing, with only just enough drive for heroics and exploration to get her into (and out of) trouble. However, no matter how skilled you are you aren't ready for a swarm of unown to rip apart the fabric of reality and throw you into an unusual new world! Thankfully, the natives are understanding and quite helpful.
The issue comes up when her Pokemon team are spread far and wide across Equestria, and don't adapt to their new surroundings quite a readily as their trainer does.

(Pokemon/MLP crossover. Rating of 'Everyone' is pending at this time. If this story proceeds in a way that makes a 'Teen' rating more accurate, I will update it.)

Both Link and Epona race to fight evil once again, however once they make it to the thing that is behind all the monsters that roam Hyrule, they get a big surprise. Once again, Equestria is threatened by evil and Link is once again called to the line of duty. Isn't he?
~~~
[NOTES]
I will add tags as I go along.
Cover image was made by Aeroflyte on DeviantArt, which can be found here, go check him out.
Now edited by these people: m2pt5 and Crescent Quills!
Based off of the Ocarina of Time timeline (which includes Majora's Mask), but takes a few aspects from Twilight Princess.
~~~

Six monsters from the monster hunter universe appear in equestria after being slain, What happens next?do they fit in? or will they be outcasts, lost in a mysterious world. Whatever happens though, this ought to be fun...

The monster was the best friend I ever had. Boris Karloff

Twilight's in some pretty deep trouble. It's bad enough that she put on a lot of weight, really let her mane go, and seems to have picked up a bad habit of chewing on anything. No, that really doesn't compare with the claws that have replaced her hooves, the fact that she can stand up to about 25 meters tall, breathes fire, and had an involuntary species reassignment spell cast on her.

Mostly thanks to Trixie, looking for means to prove herself the more powerful of the two, they've both found their ponyhood lacking due to a transformation into dragons by the Bag of Tirek. Worse yet, Trixie has fallen to his corrupting influence, and become his new lieutenant in the world, preparing to release him from his adamantium tomb.

Now, it is up to Twilight and her friends, and anypony else they can drag kicking and screaming into the fight to catch Trixie and save her from her from the taint that has corrupted her, and that threatens to corrupt the world. A tall order, to be sure; but when the odds becomes so great, the fight needs to go big, lest ponykind go extinct.

The final battle for Cybertron was fierce as the Nemesis attacked the last Autobot ship in an attempt to finally wipe out their enemies. But there were no victors as both ships were pulled into the unstable space-bridge taking them to unknown space. Although they would end up in a new world, one Decepticon soldier separated from the rest will find himself somewhere completely different. How will he adapt in this strange and colorful world? Who will he befriend? and what will his destiny be?

(This story is mostly based off the games War and Fall of Cybertron, but I will use other sources if I need to. Also I want to thank Shadow Bolt for making the cover for me.)