A compromised military operation in the Baroonda system and the discovery of a mysterious artifact in Equestria lead Jedi Knight Naat Reath and a small, battered Republic fleet into an extragalactic pursuit of a dangerous group of Dark Jedi, that results in all of them ending up in the land of Equestria. Will the peaceful citizens of Equestria be able to endure the crisis that they accidentally brought to their doorstep?

When Twilight seeks to return to the human world through the magic mirror, something goes horribly wrong. Now trapped in a galaxy far, far away and in a body that she barely understands, she seeks to find her way home. But when she's pulled into an interplanetary war for supremacy her wit, skill, and will to return home will be tested. In the end, it will come down to one decision for Twilight: Light or Dark?

After an incident with the heart of Liberty, Niko Bellic finds himself awake in an unusual hospital. He quickly learns that he is no longer in Liberty City. His rough, gravely world is about to be turned upside down.

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)

Lt. Tom Johnson must make a life or death decision. Will he jump into the magic portal with his squad or will he face the oncoming Elites? (Halo) You will find out when you read the story of Nightshade Squad. Not only does Nightshade meet lots of friends along the way, but how will they take it when they find out why they are there?
Image credit: Mackaged, on deviantART. I strongly suggest you look at his other works. In my opinion he is a great artist.
Warning: Strong Language!
Spoiler: If you do not know what Red vs Blue is then you will be very confused.
Edited by: Brandedahall

Deadpool has found himself in Equestria. He isn't very happy about being in a place that's too happy, but he is trying to fit in with everypony. He makes friends and enemies, and confuses the hell out of everything. Will he be able to find a way home?Will he be stuck there? And if so, will he be a good citizen, or bring about the end of Equestria as we know it?

"You know, I don't do that to EVERYWHERE I go, you didn't have to mention that. You're lucky you're safe behind your little laptop screen or wherever the hell you're using this from. If you destroy my image completely in here, I will not hesitate to strangle ya through the-"

Do you wish for a story or not?

"Fine."

So let it be said... so let it... be done.

While visiting his sister Twilight at her home in Ponyville, Shining Armor is accidentally transformed into a little, blank flanked filly. In order to hide her mistake while she tries to find a solution, Shining Armor must live as Twilight's little cousin Gleaming Shield. Things get worse when the Cutie Mark Crusaders meet the new filly and decide she needs to join their group in their adventures around town.

Thanks to DDRMASTERM for taking the time to edit the story

Edited by: Arcanist Ascendant

The connections between worlds are tenuous at best, and some of the "simple" truths we clutch so frantically to are little better than drift wood on the endless sea of possibility. The young knight Morenth knows this better than most.

Having reached the pinnacle of his order, he has achieved the title of Paladin. As a slayer of all that is evil and unnatural one would think his faith indestructible, but Morenth harbors doubts.

Desperately, he throws himself into battle after battle, seeking to blind himself to the truth of his world. The truth that no matter how much light he brings to bear against the darkness, the struggle between good and evil will never be won.

Meanwhile, the unicorn prodigy, Twilight Sparkle's faith couldn't be stronger.

With the teachings of her mentor and the help of her friends, she has overcome even the darkness of King Sombra. Restoring peace not only to Equestria, but to the Crystal Empire as well.

During her adventure she was forced to use a form of magic she'd only seen her teacher use once. Magic Celestia could never have guessed Twilight would have to use.

Dark magic.

Curious as to how far she can take this new power, she runs afoul and finds herself in a world that truly reflects the nature of this new magic.

A few months after the events of Super Speedy Cider Squeezy 6000, Applejack decides to officially integrate the others into her family with an Apple tradition: a long night of cider drinking.

The next morning Applejack wakes up...in Twilight's bed...with a gold band on her hoof...and a legally binding document on the bedside table...

Cover art by ThePristineEye

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And check out About Last Night: A Deleted Scene, by EquesTRON.

Subject Delta, an Alpha Series Big Daddy, has been through a lot in his life. But this is his last stand, he and his Daughter Eleanor are going to escape from Rapture. The Pairbonding destroyed, his body tired from all the fighting ... Subject Delta won't live to see the world beyond Rapture. The ending coming near, he finds himself escaping Rapture ... to only awake in a stranger place. Will Equestria be able to handle Subject Delta?

--Crossover with BioShock 2--

Author's Note: First, criticism is highly appreciated. Second, this isn't my first fanfic rodeo, but it's the first time in English. Errors will ensue, so feel free to correct me! Third, I hope you enjoy the story!

Copyright: My Little Pony: Friendship is Magic (Hasbro), BioShock 2 (2K Games), Cover Image (The BioShock Wiki).

Tags: Crossover, Alternate Universe, Human, Dark. --Will be updated--

Characters: Subject Delta, Eleanor Lamb, Sofia Lamb, The Family, Twilight Sparkle, Spike, Rarity, Applejack, Rainbow Dash, Fluttershy, Pinkie Pie, Princess Celestia, Princess Luna, Augustus Sinclair, Yi Suchong, Andrew Ryan, Shadow Stalker. --Will be updated--