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 )