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)

The Life Aura Center is one of Equestria's top medical research centers, the producer of spells and medicines that have cured many once-fatal illnesses, and they continue to produce quality technology and cures. No one wants to think that they're doing anything unethical, but Celestia has her suspicions, so she sends Twilight to investigate.

One symbiotic pairing with an alien later, Twilight realizes Celestia was right to be suspicious. Now, working together with the strange creature inhabiting her body, Twilight will have to expose the center's shocking truth. And not get killed in the process. It's gonna be a wild ride.

Now with an audio reading by Mr. Snarky on YouTube! Please give him your support!
Part 1 Chapters 1-4
Part 2 Chapters 5-12
Part 3 Chapters 13-19
Part 4 Chapters 20-25

I also have a Discord! Rather quiet right now but feel free to join if you wanna talk fics or just ponies in general! Ask me for the link if you want in, I had to remove it because of too many spam bots.

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Arceus, God of Pokémon, Master of Creation and Leader of the Legendary Council has made Equus a new home for his Pokémon hoping to give them a fresh start and escape the Darkness and evils of Earth and protect his children.

But little does he know that Equus has been in the crosshairs of Darkness for One Thousand Years.

Oryx, The Taken King, First Navigator, Lord of Shapes, and harrowed God has come to Equus to avenge the death of his son who was killed by the Princesses. With his army and his fleet at his disposal he arrives at the planet only to find resistance in the form of creatures known as Pokémon, united in an effort to defend their new home.

But what Arceus and the people of Equus don't realize, its that Oryx is called the "The Taken King" for a reason.

And the answer will horrify everyone involved.

Non-Canon Wayverse Crossover with Destiny.

Takes place after the end of Book 1 in the Wayverse

Note to Pokemon fans: knowledge of Destiny is not required to read this. I'll take care of that :D

Prologue and Chapters 1-3 Edited byScript and metallusionsismagic

New Editor: tdnpony

EDIT: Made the Popular Stories list!

The events take place after the Main 6 defeated Discord, while the other side, Ash has just finished his adventures in Alola. The two worlds intertwine, making the Ash Ketchum and his partner Pikachu cross paths with Twilight Sparkle and her friends.