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)

An MLP/Warhammer 40K Crossover

The Iron Warriors 38th Company has landed in Equestria, entrenching themselves like a barbed hook. They hunt the aliens of the Tau Empire, intent on destruction and pillage.
A small squad is dispatched on a reconnaissance mission, only to find that there is intelligent life on this world besides the feuding space-farers.
Will these improbably adorable and friendly equine aliens turn the damned warriors of Chaos from their blood-soaked path, cleansing them of their dark legacy with the magic of friendship and harmony?

No.
No, that isn't happening.
EXPLOSIONS!!

(Dark humor warning; limited grimdark themes)
(Cover art by Nicholas Kay)
(This series now has its own TVtropes page!)
(This story is a contestant in the Tournament of Canterlot, a charity event to raise money for Syrian refugees! Go here for details and donations!)
(Featured on Equestria Daily 8/20/15 )

This story is a sequel to Stardust

Times are changing for Equestria as Twilight’s return brings with it news of people and cultures from beyond the peaceful world everypony knows. Aid and volunteers are freely offered to help the besieged humans of Earth because every Equestrian knows that’s what good friends do. Unfortunately, making friends can also have the unintended consequence of making enemies.

When the monsters besieging the humans strike at Equestria with a level of brutality not seen in over a thousand years, the cry for help is sent to all the kingdoms of the world. Honored allies step forth to fulfill ancient treaties and oaths. Enemies, old and new, bury their grievances. An alliance never before seen in Equestria will be created to combat the monsters from the void.

And because of these events, a grim but welcome sibling to the XCOM project is born.

(XCOM/FiM Crossover)
(Sequel to Stardust, which I recommend reading before starting this. Fortitude Amicitia and Broken aren't required reading but are supplemental to the storyline)
(Gore tag for blood and violence)
(Alternate Universe tag because of the divergence from canon that Stardust has caused)
(Uses elements of Season 4)
(Coverart produced by the amazing Carnelian!)
(Many thanks to Arzoo, BradTheBrony, Vandenbz and Setokaiva for prereading!)
(As of 03/07/2016, the prereading team consists of Arzoo, BradTheBrony, Noble Cause and Metallusionsismagic!)
(Complete with it's own TVTropes page as part of the Stardust continuity. Could use some updating!)
(Character tags will be added as chapters are added!)
(Featured 5/12/2014! Thanks folks!)
(Possible spoilers in the comments! BEWARE!)

Life had been peaceful in the world of Fœnum. The inhabitants of this world – furry, four-footed, hooved – had thrived for generations, creating culture, building societies. They lived happily, with sweet, grassy pastures at their disposal and great, expansive fields to gallop across. They were free. But everything changed when the fire nation attacked

A chance magical occurrence from Twilight and Oleander has thrown the time-space continuum out of whack, throwing the universes of My Little Pony and Them's Fightin' Herds together (And BFDI, because why not). And the threat of the predators still looms on ahead, threatening now not one, but both dimensions (And BFDI)! And with the ponies no longer having a reliable insta-kill option, what will befall them?

Join all your lovable ungulates (and dragon) (and random household objects) as they race against the clock to save Equestria! And Foenum! And like three people from BFDI! Man, is this confusing.

On hiatus until Story Mode: Chapter 2 releases.

Not long after Equestria managed to discover and contact the faraway continent of Foenum, Princess Celestia received a visit from six individuals said to be 'Champions of Foenum'. After telling their intentions, the princess allows them to explore Equestria.

Though, when these champions meet certain ponies, they realize that they share something in common, even though they never meet each other.

Edit (27/03/2021): Featured!? Holy smokes!

Edit (01/04/2021): Featured again!? That's not even a lie!

There are surprisingly not many pictures of the mane six and the TFH characters together.

Keep in mind that the story of TFH's main six may not be accurate to their original source, as with the state of the game at the current time, not all the information of the champions are revealed yet, so I kinda have to make my own version of their story.

Also, the mane six's story is also slightly altered to fit some of the settings of Fighting is Magic, where their main enemies are changelings.

Cover art source: https://pembrokewkorgi.tumblr.com/post/131805131444/thems-fightin-magic

This story is a sequel to The Dresden Fillies: False Masks

It's been a while since the girls have seen their good friend Harry Dresden. Discord escaped, Luna attended her first Nightmare Night, the Royal Wedding was crashed by hordes of changelings, and Pinkie Pie threw a statistically improbable number of parties. They tried inviting Dresden, but between his new job and new apprentice, he always claimed to be too busy. The solution was obvious; if he couldn't come to his friends, they needed to go visit him. Besides, they say Earth is lovely this time of year. What could go wrong?

Roseluck's life was somewhat boring, stuck in a rut. Opening the stall she shared with her foalhood friends at the local Ponyville market, serving customers, shipping large flower orders to their destinations, tending to the garden, taking inventory, paying rent... Although she loved her job as a florist, she craved some excitement in her life.

But luckily she has a trip to Manehattan with her friends for a decorative flower contest, something that always got her out of her routine. However, when she gets there she notices something strange, many ponies are behaving strangely, they are staggering, they have clear signs of lack of sleep, and they almost seem to have no energy. Driven by curiosity, she plunges headlong into a conspiracy that threatens all of Equestria, perhaps the entire planet.

But luckily, not only has she stumbled upon this conspiracy, she has also gotten in the way of somepony who can stop this whole mess. He calls himself the Doctor, and it's clear to Roseluck that he's the strangest pony she's ever met, but he also seems to be the most extraordinary. Will Roseluck and the Doctor be able to protect Equestria?

This story is a sequel to The Dresden Fillies: Strange Friends

Almost a year has gone by for Harry Dresden since he left Equestria. He'd have written, but between saving his newly discovered brother and destroying a scourge of vampires he's been a little busy. Then out of the blue he receives a strange letter from Twilight asking him to return. With no cases at the moment he eagerly accepts, but his friends aren't the only ponies expecting him. There's been a lot of rumors since his last visit and some ponies aren't too keen on seeing him come back.

A sequel to The Dresden Fillies: Strange Friends.

Argyle Starshine returns to Maretime Bay, surprising Sunny and her friends who were under the impression that he was dead! Understandably, Sunny is thrilled to be reunited with her father. Izzy Moonbow is happy, too, but can't shake the feeling that something is off about Argyle. And when Sunny begins acting abnormal, Izzy's concerns only grow.

Written for the Generation 5 Bingo Writing Contest. My prompts were: Argyle, Izzy, G1/2/3 Character, Maretime Bay and Changelings

You can find other entries in the contest here.

Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?

"In short, it's a story of friendship and plasma rifles, with the emphasis on the friendship. The characters are well written, the XCOM setting is fleshed out very well, and the story is compelling. If you love XCOM, you'll love the story, but even if you've never heard of it, it's more than worth giving the first 3 chapters a read.

There's excellent action later on, but the real strength lies in the collision between the friendly and naive world of Twilight Sparkle and the desperate world of humans fighting a losing war for survival and willing to do anything to turn the tide."

--Arzoo

(XCOM/FiM crossover)
(Cover art commissioned by a friend and created by the magnificent FoxInShadow!)
(Original cover art by the amazing Carnelian can be viewed here!)
(Gore tag for blood and some violence)
(Many thanks to the studius OminousTen, Arzoo, xXFluttershyForeverXx and finally Setokaiva for giving my rambles a once-over)
(Now with it's own TV Tropes page! Get to tropin' folks!)