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)

It was just another day in school for Fluttershy in Ponyville High. Conflict is brewing between two races, The Humans and The Trans-mutants, tensions are high, and prejudice to one another is rising higher than before. To make matters more tense, some of the Trans-mutants are being allowed to walk among them as well as attending the same schools. Fluttershy will cross boundaries that few would dare cross.....Making friends with one.
(A Humanized crossover fan fiction of Godzilla and MLP FIM. If you are familiar with "The Arrogance of Man" (http://www.fimfiction.net/story/220838/the-arrogance-of-man), then be aware that this is an alternate universe for the story). Sex tag is mostly for dialogue that may be deemed dirty at certain points, and intimacy. No sex scenes, keep this in mind. Cover art is by me, and props goes to Moongaze14 and ThePMB-Brony for proofreading this story. Thanks again guys!

Breaking the Walls Arc: In a world of humans and mutants, Fluttershy befriends a boy, Gojira Takeshi Jr, who has a gruff and pessimistic attitude, with a reputation to boot. Sometimes, it takes kindness to uncover what's beneath the surface. (Chapter 1-15)

Sins of the Father Arc: With his father back in his life, Junior finds himself caught up in situations that turn his entire world upside down. In comes new friends, and new revelations. From the shadows, enemies plot to bring chaos. And somehow, the Takeshi lineage is at the center of it. (Chapter 16-72).

Celestia has never used her full power.

Ever.

But that might be about to change. Chrysalis has contacted her and requested a meeting out in the middle of nowhere. Celestia expects a trap. In fact, she's hoping for it.

Featured: Because you guys are way too nice to me. Thank you all!

Now with a Spanish translation: https://www.deviantart.com/spaniard-kiwi/art/Un-mundo-de-fosforos-923171362

Octavia Melody. Despite her youth, she is a very well-behaved little girl with a passion for playing the cello. Her step-sister, Vinyl Scratch, is a very free-spirited, playful, and rambunctious little bundle of trouble.

Despite the vast differences between the two of them, they're still closer than step-sisters could ever be. Even now, when they are still in their early years at elementary school, these step-sisters have quite some stories to tell...

Pinkie Pie is being tormented by horrific nightmares. Unable to deal with it by herself anymore she seeks out Twilight's help, but will it have been the best decision when she finds herself alone in an abandoned, fog filled Ponyville?

Sequel: http://www.fimfiction.net/story/4676/Too-Shy-for-a-Rainbow

There have been a LOT of high-quality readings of Silent Ponyville, but this one is my personal favorite:
https://www.youtube.com/playlist?list=PLGh01rbB4o3xoSV7a6Omc-UJROXHRZ1Hv

In an unremarkable city, in an unremarkable hospital, to two unremarkable ponies, a filly was born. A filly who was all too remarkable. A filly who radiated Destiny, and Adventure.

Her parents, however, liked their unremarkable life, in their unremarkable city, and wanted nothing more for their little filly than to have a nice, normal, unremarkable youth. So whenever Destiny or Adventure reared their heads, they made sure to nip it in the bud. Magical portals, foreign princes, time travellers and mysterious salesponies of magical musical instruments all got the same answer:

Nope.

Based on the Nope: The Anime joke (original posts) that went around on Tumblr some years ago. Expect silliness.

Covert art based on a picture by greyscale / Theponysketchguy, edited by me to change her hair and eye colour and make her look younger.

Spanish version:
Un poni llamado Nop on DeviantArt, translated by SPANIARD KIWI.

Deep in the Royal Library is a book. A terrible book that is said to send whoever reads it mad. A book so dangerous that it has to be hidden away and secured with chains to prevent it from ever being opened.

A book which has just been accidently checked out by Spike on behalf of Twilight Sparkle.

The Star In Yellow is rising once more, and only Rainbow Dash and Spike can save Twilight before it's too late. Ideas live forever. Ponies do not.

This fic is loosely inspired by the 19th century story 'The King In Yellow'.

This story takes place in an alternate universe (they are humans, not ponies).

Twilight Sparkle is given a Scholarship to attend Headmistress Celestia and Vice Headmistress Luna's Princess Preparatory, a school for young Princesses in the making. This is because her brother, Shining Armor, is attending the school's "brother school"; Prince and Knight Academy. Which is led by Headmaster Thorax and Vice Headmaster Pharynx. Shining attends because he is courting Princess Cadence, who is like Twilight's sister. Her brother, Spike, is with Shining at Prince Academy. Twilight Sparkle meets six other girls, who are born Princesses. They help her to succeed in the Royal School. But there are many obstacles they must face.

Meanwhile, at Prince and Knight Academy, Shining Armor and Spike have made friends with five certain boys. When they are asked to have a joint class with the ladies of Princess Prepratory, they fall in love with certain girls. Together the boys and girls strive to complete their years and graduate, working together to solve problems (and fall in love while they're at it)

(boys are in the story a medium amount but there's not enough number of tags to include them)

Important Ships in story:
Soarindash
Shining x Cadence
AppleSpike
Rarity x Fashion Plate
CheesePie
Twilight x Star Tracker
Fluttercord
Starburst (Starlight x Sunburst)
Sunset Shimmer x Flash Sentry
Spitfire x Fleetfoot

This story started with a single realization. The voice actor for both Snails and Ranma happened to be the same person.

Snails 1/2 is a Ranma 1/2 spoof. Not actually a crossover, this is the story of Snails dealing with a Jusenkyo style curse. When hit with cold water he... becomes a filly. As if that wasn't horrifying enough, he quickly finds himself caught between rivalries, forced into competitions, and now he feels like he is developing a severe phobia of water.

With artwork by Alkarasu and edited by Swyrl, this is a story made as a pure slice of life comedy in the style of anime.

For the continuing story, join us in Snails 1/2:The Perfect Stallion

"You can be a hero!"

Twilight Sparkle wants to be a hero. She didn't expect the most powerful hero in Equestria to lend her a hoof. She's now set on the path of legends, but it's not going to be an easy one.

An MLP x My Hero Academia Crossover.

Edited by Emtu

Gore tag because If you know the source material, you know what's in store for Twilight