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)

Hope is the faith of the young. Losing everything she holds dear, Puppysmiles embarks on the adventure of her life to find her mother, her hopes of meeting her again driving her through the horrors of a world not of her making. Too bad the Wastelands doesn't care about hope.

On a dark night filled with even darker magics, an insane cult attempts to give Nightmare Moon a body and life of her own, utterly separate from Princess Luna. But, when the spell is interrupted by Celestia, something unexpected is created.

Now, a little black alicorn filly named Nyx finds herself living under the care of Twilight Sparkle, only to be haunted by memories and emotions from her past. Is she Nightmare Moon reborn or is she simply a doppelganger with a soul and mind of her own? Can Twilight Sparkle protect Nyx from those who refuse to see past her dragon eyes and black coat?

Or, will Nyx be forced to inherit the sins that may not even be hers and become the greatest evil Equestria has ever known?

The Planetary Map; A bronze ball of inscriptions, when activated, the device shows a gargantuan map of the entire galaxy, every nebula, sun, planet, blackhole, you name it, its all there. Stories of the so called 'Treasure Planet' have been told by cults for generations.

But now, they have a map of the whole universe. Is the map a fake? Is a real planet, where if they find it, they will be rich beyond their wildest dreams? Who knows, you might just keep reading and find out.

[All Main-Cast will be the crew, captain, chef, etc.., it will workng differently than the movie.]

Twilight Sparkle, Arcane Mage, knows that there is some truth to the story of Nightmare Moon, but her mentor, Princess Celestia, dismisses the matter in a heartbeat. She sends Twilight to the town of Magiville to oversee preparations for the Summer Sun Celebration, much to Twilight's distaste.
Unbeknownst to her, the darkness is gathering in Mystica. Assassins lurk in the shadows, Undead gather in the forest, werewolves sharpen their claws, and criminals and mercenaries prepare themselves.
To win the coming battle, Twilight will have to rely on her wits, her magic, and the five mages she's been saddled with. No matter how much they annoy her.
Rated teen for violence and language. Humanized, action-y. Based on the first two episodes, with some large changes made.

After a demon summoning spell goes wrong, a magical 'void' is created on the outskirts of Ponyville. Celestia sends her prized student to investigate and to prepare for whatever this 'void' means for the future of Equestria.
Something is coming, and Equestria will never be the same.

Part 1 of the Titans series. This will update with at least one chapter every Friday.

As I am tired of answering the question. No, I repeat, NO this is NOT a TCB story. That idea was last perpetrated by people Like Hitler, Hirohito, Saddam and would be considered a serious crime by the standards of both parties.

We all know that Twilight Sparkle went back to her own world after she defeated Sunset Shimmer. They know it too. So why is it that on their senior trip they see a girl that looks exactly like her?!

Cloud Kicker might just have the wildest life of any pony in Equestria. Marvel at the insanity that is her life, and laugh at the suffering of her poor beleaguered best friend, Blossomforth. And maybe, just maybe, there's more to her than just the lovable sex maniac everypony thinks she is.

This is a semi-sequel to "The Incredibly Dense Mind of Rainbow Dash." Not really a proper sequel, since it's focused on Cloud Kicker and Blossomforth instead of Rainbow and Pinkie, but it's in the same continuity. So I guess that makes it a follow-up-side-quel story. Or something. You don't need to have read "The Incredibly Dense Mind of Rainbow Dash" to read or enjoy this, but you ought to read it anyway, just because.

TvTropes Page

The central story of the Winningverse.

We got a tag for Cloud Kicker, but Blossomforth still deserves one too.

Rainbow Dash struggles to figure out why Pinkie Pie keeps acting weird, and seems so happy about spending Hearts and Hooves with hanging out with her, while also puzzling over the fact that Cloud Kicker and Blossomforth seem to be going out of their way to help the two of them enjoy the day.

Cloud Kicker and Blossomforth need to have their own tags, because they're awesome characters who deserve to have more stories written about them.

Has a semi-sequel-follow-up-side-story:"The Life and Times of a Winning Pony."

Princess Celestia had envisioned a much more joyful reunion with her sister, after a thousand years of separation. While seeing each other was a tearful event, the sibling she once knew is now different. Luna had become...cold. It feels as though something is...missing.
Fortunately Celestia knows what will cheer her up; a little reminder of the days long gone by. Perhaps one cold, could melt another.