Please do check out the Reading List by Lance Omikron to navigate the Amalgam Universe most clearly

A massive war of titanic forces is taking place in the Kaiju's world. However, when two faction's leaders, the current Godzilla and his 'brother' Xenilla duke it out; humanity unleashes its most devastating weapon. Something beyond comprehension occurred and the boundary that divides worlds, if only for the briefest of moments, was torn to shreds. New forms are taken, new bodies assumed. But old hatreds die hard. But how well can hatreds continue in the world of love and tolerance? Especially with its own demons follow it there?

Godzilla Franchise by Toho Company Ltd.
My Little Pony is owned by Hasbro Studios.
This is a non profit fan-work and I claim no ownership on the IP itself.
Story created by Tarbtano
Co-created and Contributed by Faith-Wolff and Skylark8756

HOLY SHEETZU WE GOT FEATURED! THANKS GUYS!
6/27/2014
Now on TV tropes (Thanks Raidrik, VampyGirl; Lance Omikron, Ultimomant, and ZimFan!)

Kaiju Cast:

Godzilla a.k.a Gojira
Xenilla
Mothra
Anguirus
Rodan
Destroyah

[Character copyright of Toho and Daiei Company, artwork property of Matt Frank]

(for any G-fans, Xenilla is the kaiju you may know as Spacegodzilla. I changed the name because I got quirked about typing it repeatedly and am writing the story so it can at least be understood by just an MLP or just a G-fan; and thought it get very confusing that one character's name was just another character's name with an adjective. Also... don't pretend it's the most imaginative name Toho has every made)

This is a Fallout Equestria (primarily) and Terminator crossover.

As the war between Equestria and the zebras pressed on, many members of the Ministries conceived of desperate strategies to end it through magical and technological creations of questionable nature. One of these was Project Infiltrator, a top secret project of the Ministry of Awesome. It's goal: to create a super spy that was the perfect blend of pony and machine. But just as its first subject was ready, the megaspells dropped, destroying Equestria and creating the Wasteland.

190 years later, Crystal Eclair awakens in a world of ruin and violence, completely clueless as to what happened to Equestria and herself. Her confusion grows into horror as she discovers that she is no longer a pony, but now a cybernetic zebra. With no other choice left, she sets out to find answers to her predicament. How will she handle the truth if she finds it? Will she find friends who can help her in a world that trusts no one? And what if those who have done this to her are still out there, eager for her to serve a new sinister purpose?

PS. This is not a Prequel to Broken Steel despite what a couple of websites that link back to this story say.

(Chapters 1 to 12 Edited by Alycorn~(CF), New Editor Double R Forrest. New description credit to Double R Forrest )

This story is a sequel to A Different Perspective

Both the House of Path and Herd Path enjoy strong growth in the years following their establishment. Like all such things though, they both have their highlights and lowlights. These are vignettes in the lives of the children of Twilight, Path, Free, & Roseclaw, from foals to young adults.

This is a series of stand-alone stories of events that occur after the events of A Different Perspective, which I strongly recommend that you read first.
My collaborator, AlaskaIsCold, has written some of these and I mostly just edited them.

The Cutie Mark Crusaders have always lived in the now, getting what they think needs to be done as a soon as possible, executing their plans just so they can move on to the next one right away, not thinking about the consequences till they’re right there in their faces. But when an attempt to earn their cutie marks goes too far, Sweetie Belle and her friends must face a horrible reality that sends their world into darkness and fear. How will the truth be uncovered and what will be sacrificed to undo this nightmare?

This story is a sequel to Steel Soul

Sweetie Belle has discovered a secret. She's spent a few months keeping it to herself, but the nightmares she's had have convinced her it might be time to reveal it.

Sequel to Steel Soul.

Applebloom just wanted to spend a day with her friends, crusading for her cutie mark. Instead, she found something even deeper and more troubling about herself. Turns out she's not even a member of the Apple Family by blood. In fact, she's not even truly native to Equestria! She's an alien! An alien robot no less!

Now Applebloom will have to deal with the reality of her origins and try to cope with them and her newfound abilities as she moves towards her future; a future that just might never come to be if her new foes have anything to say about it. Decepticons are, after all, a monstrous cabal.

Now, it's up to Applebloom to light Equestria's darkest hour.

Cover image credit goes to Inspectornills

"All my life, I've wanted to fly
But I don't have the wings, and I wonder why
I can't break away..."
Most pegasi figure out flying easily enough. Heck, most of them figure out how to do it before they even get their cutie marks.

But not me. I couldn’t do it, no matter how hard I tried. I couldn’t even hover. Not for more than a few seconds, anyway. And not even Rainbow Dash, the greatest flier in Equestria, could seem to help me. We tried everything, and I failed every time. Day after day, I tried – and day after day, I failed, until finally I was ready to just give up. I’d never be able to do it. Nopony would ever be able to help me to fly...

...until one day, somepony did.

Twilight Sparkle never was a Unicorn and she didn't even know it.
What happens when her true heritage comes to light? Will she willingly embrace it? Or will she be forced to?

Beware of spoilers in the comments!

Edited by uTTerAbsurdity, Zervziel, Stormwatch and Gwenio

Cover art by the talented Cartoonlion and colored by the equally talented Stormwatch, original can be found here

Click here for the Tvtropes page

During the Discordian Era, Chaos ran free, allowing many monsters to establish solid footholds. Footholds that were lost when Celestia and Luna cast down Discord and took his place as the rulers of Equestria. Now, many thousands of years later, the Elements of Harmony, the very same tools that struck down Discord, belong to six individual ponies. Six vulnerable ponies. An ancient draconic vampire begins his campaign of revenge, uncaring of who is caught up within it. His first target? The Element of Magic, student of Princess Celestia, Twilight Sparkle.

Art by Archonix Source is in the link, and he does do commissions.

The Great and Humble Trixie Lulamoon's reputation could not possibly be any worse, but that is about to change.

Following the disaster with the Alicorn Amulet, Trixie turns herself in to the authorities to account for her crimes. In penance, she is tasked by Princess Luna with the defense of Hollow Shades against a shadowy and unknown foe.

Trixie will have to draw upon every trick and every scheme she knows just to survive. And when faced with a fate worse than Death, she will have to prove there is more to her than flash and spectacle, and learn just how far her magic can go.

And learn how to Rise.

A Side-Story of The Code's Apprentice and The Code of Harmony
Many, many, Many thanks to Hooves McCoy
and The Cacophonous Muse for their aid in editing this story.