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 Lone Wanderer has been known as the man who shouldered the nightmares of every man, woman and child in the wasteland, so that they may live. But when the Wanderer was once again abducted by aliens, he found himself falling, quite literally, into a whole new wonderous world, untouched by the horrors of nuclear devastation.

He has been facing other people's nightmares constantly for almost a decade, it was high time he was allowed to wake up.

Meanwhile, the ponies of Equestria are baffled by a strange object that fell from the sky.

Fallout/FIM crossover. HiE. T for violence and some language.

Now with a TVTropes page!

Shortly after the theft of Twilight's crown by Sunset Shimmer and Twilight's departure, Equestria's First Human, Connor Powell, goes through the mirror into a world he is most familiar with.

(Another story branched off of "Equestria's First Human")

(An "Equestria Girls" fic :3) (NOTE: Until a proper cover art is made, I will leave it blank for a while. Guess I forgot to draw one :3)

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!

The first story in The Journey of Graves.

Ponyville is getting ready for the arrival of Princess Celestia's marshals, elite of royal guard and travelling heroes of the people. But in all the hustle and bustle of party preparations, a lone traveler slips into town, a young man with business concerning Twilight Sparkle. What that business is remains to be seen, but you can be sure Ponyville won't make it easy for him.
After all, where would be the fun in that?

CANCELLED

A botched viewing spell has sent Twilight Sparkle to Earth and into the care of Kyle West. Having been turned into a human, the local species, Twilight Sparkle relies on her host to help her as she finds a way back to Equestria. And, in the meantime, she decides to learn about humans and the world they live in; the good, the bad, the beautiful and the ugly.

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Trixie has gained national... um... fame? I suppose more ponies would call it notoriety, but it really is quite relative if you think about it. Anyway, Trixie Lulamoon is known all across Equestria for telling the most fantastical tales, preforming the most incredible magic shows, and being the most self centered, power hungry, show off in all the land! Now, Trixie is all for the fame, but a mare has got to eat, and apparently ponies don't like to hire someone who managed to take an entire town captive, molest its citizens, and walk away a free mare without so much as an apology for punishment... someponies just don't know how to look past the surface I suppose. So, in order to start a new beginning, and find some actual freedom from her past, she has traveled far and wide to find... uh... just start reading already, would ya?

(Third person. Pony on Earth. A bit of warning, some parts may seem serious, but they are not. If you read this fic, and start to take things seriously you will either be offended, disappointed, or have the time of your life. This fic was made so I could have fun, and entertain others that like something a bit different than the usual HiE fics.)

Inspired by her many trips through the Everfree Forest, Twilight gets an idea for a book. With a little help from her friends, however, what began as a single passage quickly evolves into an entire universe, with the Mane 6 as its goddesses.

The Helicoprion, a long-lived genus of shark-like cartilaginous fish that went extinct millions of years ago. This predator certainly was a strange one, seeing how its lower jaw was basically a mix of a fruit roll-up and chainsaw. I make a living studying fossils, and this guy certainly takes the cake for the number one in the weird factor. So imagine my surprise when I inexplicably turn up in Equestria of all places. As a Helicoprion. Guess it's just one of those days.

You can thank Csquared08 for the idea for this story. And I will get that seal of approval, one way or the other. Also to my kickass editor, Linkerman! Thanks for all the help, dude!