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)

A close encounter with a category three Kaiju leaves Midsummer Night, a Mark-II Jaeger, in the inky depths of an unknown ocean. With no communications or navigation available, the pilots, Shane and Michael O'Connell, are well and truly out of their element.

Good thing they accidentally brought something with them to liven up the party,

Pacific Rim crossover

Art by: Zeiram0034.
Edited by: Pixel brony.

Now with a Tvtropes page!

Twilight Sparkle was merely sent to the caves beneath Canterlot in canon, but what if Chrysalis, who'd recieved a large power boost recently, and who'd realized that putting Cadance and Twilight in more or less the same place might be a bad idea, decided to use a spell she'd learned a long time ago, but never had the power to pull off. Twilight was sent to a parallel world. In this universe, or perhaps I should say multiverse, parallel worlds come in two flavors. 'Line' worlds, which are like parallel lines, never touching, even if they're an atom apart, and 'Mirror' worlds, which are essentially alternate worlds that closely resemble their counterpart, save for a couple differences. Now on a quest to return home, what adventures await Twilight? Note that this is a crossover, and I claim nothing in here for my own. I will mostly use video games and shorter anime as the worlds she'll visit, though OCs might exist.

Snakes are beings of cunning and wit. Seviper, or Commander Sev of the PLA, is no exception. His cunning mind has been at work, plotting and scheming to strike back at the human oppressors.

And he would have too, if he didn't find himself and his army scattered about in a foreign world. And what's worse. There are no more humans to fight....

Guess he'll have to help the ponies, or something to keep his mind off of things.

Side story of 'A New World, a New Way'. Go check that out now.
TVtropes
(Please feel free to contribute to this fic's part.)

One Piece X MLP Crossover

A emergency trip to Zecora's leads Fluttershy to find a strange pony with a straw hat. Unfortunately, he scares Fluttershy off with his talk of eating other animals. The strange pony's arrival in Equestria sets off a chain of events that threaten plunge the peaceful kingdom into an all out war. Twilight and her friends, along with the new pony may be the only ones who can unravel the mysteries that surround Equestria and save it from falling apart.

Now with TV Tropes!

New Cover Art by Droll3

Turned into a Pokemon, John, a International Police officer, find himself in a world of Ponies.
However none of his skills will prepare him for what he has to face. For a darkness looms all around the Crystal Empire, and it is up to him to both save Pokemon from this new world... and to save the world from this Darkness.
This story is a spin off to the "A New World, A New Way" by zeusdemigod131

Please leave a like if you enjoyed my story. It really helps my progress.

Chapter 1 to 11 Pre-read by: Dragaen

This story is a sequel to From The Gates

Taking place three months after the events of From the Gates, the Elements of Harmony and the former homunculi were enjoying their new lives and what has been laid in front of them. But after a large accident at the Grand Galloping Gala, all sorts of chaos will unfold. Will the Elements succeed a third time with the help of the homunculi, and will Greed finally know the meaning of Generosity? Stay tuned for more!

Future chapters edited/proofread by Pixel brony and Dawn Flower.

My Little Pony: Friendship is Magic is copyright of Hasbro
Fullmetal Alchemist: Brotherhood is copyright of Hiromu Arakawa/ Hiroshi Onogi/ Square Enix