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)

Nearly two hundred years have passed since the war that ended civilization. Stable 115, located in the once vibrant prairie lands at the edge of Equestria, is home to a young unicorn mare and her precocious filly. Life in the Stable is about stability and routine, and mother and child find comfort from this monotonous existence in each other and their friends.

Life in the Stable is about to change...

Inspired by Fallout: Equestria by Kkat, and Fallout Equestria: Project Horizons by Somber. Author suggests having read Fallout: Equestria before venturing into this tale.

Update 11/04/2012: To prevent confusion, an explanation about how the chapters are named/numbered. I essentially have the story split into several acts--each act will have a named chapter that precedes the number chapters and are a somewhat separate tale, but will eventually tie into the main story. If I ever manage to finish this (or you figure it out way, WAY before then), then it will hopefully make sense.