Tiberium. The infamous green crystal that destroys entire worlds in its wake of global proliferation. It has been a little over a century since the Tiberium threat was first wiped out on Earth, and with it, the primary vestiges of the Brotherhood of Nod. When the GDI advanced humanity to the stars, they found that Earth had not been the only target of the alien Scrin: dozens of other worlds had already been claimed by Tiberium, and the Scrin returned in full force, attacking human colonies across space, stopping human expansion. To fight back, the GDI undergoes a reformation to become the Interstellar Defense Intiative (ISDI) and enacts the Hallman Directive, designed to stop Tiberium spread wherever it may be; such a protocol brings the reincarnated ITC Methuselah to a planet being ravaged by the green crystal, and the forces under Commander Martin Alexandra deploy to stop the threat.

Crossover Material: Command and Conquer - Tiberian Series/MLP
Rated Teen for Graphic Violence and Language

Scar the gnoll and the newly-formed pony squad arrive in the Griffon Kingdoms, eager to hunt the hated Izelim from their hiding places but unaware of what sinister plans lie hidden in the dark.

While the ponies and griffons focus on the present and what the future may bring, the gnoll finds himself faced with his own past as their journey takes them closer and closer to his old, forgotten home.

This is the second part of The Reader. Reading the first part is not necessary, but is highly recommended.

The storm is breaking on the Horizon.

It's been two months since the battle against Nightmare Moon. Luna is recovering, Celestia is busy turning the government back into a diarchy, and the Mane Six have returned to their lives. All seems well, but when Celestia discovers that half of the power of the Elements of Harmony have been transferred to each of the Bearers, she decides to send thirteen mysterious members of the Royal Guard to monitor them as they manifest and develop their new abilities.

The sins of a forgotten war still linger, and an ancient evil lurks in the shadows, just waiting for the right time to strike. The Mane Six suddenly find themselves once again at the heart of a conspiracy to bring about Eternal Night, and only by awakening their powers and realizing their full potential can they do anything to stop it. Friends both old and new will help them along the way, and an unseen force will guide them as it seeks to right a wrong made thousands of years ago. The Bearer's journeys will take them outside the borders of Equestria and into the world beyond, and when they return, they'll have the power and experience necessary to save the world and bring about balance in all things.

The Powers of Harmony TV Tropes Page (SPOILERS)
The Powers of Harmony Art

Thanks to Wildy71090 for the cover pic.

When a rare magical artifact is stolen from Celestia's Academy for Gifted Spellcasters, her prized student Twilight Sparkle is determined to take up the task of getting it back... even though Celestia doesn't seem to want her to.

Part I of the Legend of the Six series. This story features humanized characters in a fantasy universe that draws heavily on the mythos of FiM to create a whole new adventure. I hope everyone has as much fun reading it as I did writing it, ^^

Cover art used with permission of the amazing QuizzicalKisses

After Spike's growth spurt, Celestia decided that its time for the young dragon to be taught what it means to be a dragon. So she contacts the distant universe of Avalar and asked Spyro to teach the young drake, which of course Spyro accepts. Now Spyro must deal with training a dragon who doesn't act like a dragon, keeping the populace of Ponyville under control, and fighting off the remains of the Dark Master's forces who have somehow followed him. Luckily he's got Cynder and Sparx alongside to help...right?

EDIT: Very late in saying this bu thank you everyone for getting this story to be featured. Means a lot to me.

Basically this is a T-rated crossover that takes place after the events of Dawn of the Dragon. I should mention that this story will contain spoilers for anyone who hasn't played that game. Of course, I don't own anything except for this story.

After a mysterious and widespread spell causes ponykind to vanish, Fluttershy is left behind to cope with what the future has in store for her and the remains of Equestria.

In a matter of days, the once-prosperous nation begins to descend into a harsh and unforgiving place. While cities crumble around her, Fluttershy finds herself living in a land rife with dangers and heartbreaking reminders. With nopony to turn to, Fluttershy is forced to learn to fend for herself, discover what happened, and, if possible, find a way to reverse it.

Survivor Shy is an illustrated story following Fluttershy in the weeks after a magical cataclysm. While the last pony relives her past, readers are offered a vivid glimpse into Fluttershy's mind and are led on a harrowing journey through the ruins of Equestria and beyond.

Story branches out before Season 3 Finale.

In-progress Reading by Finish Line available
In-progress Russian translation by Papilion_star available.

The Songbird, protector of the lamb of the flying city of Columbia was thought dead. Though as it would soon discover, his charge was not the only being able to open the mysterious tears. In the forest of this new land, he finds peace with the native animals. However, the urge to protect something, anything, would soon drive him to respond to the cheerful whistling of an equine with a penchant for protecting creatures like him, no matter how foreign they appeared.

No game spoilers, and the chapters that may contain vague spoilers are marked with a *
Contained within are the following characters from Bioshock Infinite: Songbird and the Luteces.

"What happened?"
"What is going on?"
"Why are we Pokémon?"
"Why are we in Equestria?"

So long story short, a brony and pegasister are sent to Equestria as Pokémon and they don't know how it happened or why. Now they must travel through Equestria to either find their way home, or live out the rest of their lives in a new world in new bodies. And only one of these questions will be answered.

"Where is Fluttershy with the cuddles?"
"..."
"Don't look at me like that, I know you want one too."
Probably going to be that one.
*****
Edited by: BronieMan305
Thardoc
halo003qd
Pre-read by: psychicscubadiver
Tank you Koru Konsui for helping me think of a name for this freakin' story.

The Canterlot Caverns are a strange and enigmatic place, untouched and forgotten by pony-kind for centuries. So when a strange metal object is unearthed in their depths, it's up to Twilight Sparkle and Lyra Heartstrings to discover the many secrets it holds.

Together, the two of them will have to do their best to understand the remnants of an ancient civilization, and decipher what remains of Those Who Came Before.

The cover-image is a cleverly edited stock image, which was modified by the stupendous Corvo.
Proofreading was performed by the equally fantastical writers:
Timetraveling Pony (Who started as a proofreader when Cloud was writing this. Hats off to him for being dedicated and staying on as a proofreader for me.)
DustyPwny
Tidal
Superluminous
Night Spark
PhiliChez

And a special Thank You goes to The Sentient Cloud for allowing me the honor of continuing this great story after he retired from writing fimfictions.

As it turns out, this story is eerily similar to Lyra Heartstrings and the Hand of Man. Due to their similarity, I feel that it would be appropriate to give said story a mention.

Officially complete!

Trouble is brewing in Equestria, and Spider-Man is summoned to save the day! However, he takes the form of a pony upon his arrival and slowly starts to lose his powers. Now as Peter Pony Parker, he must become Equestria's new hero as the Amazing Spider-Mane, but with past failures haunting his mind, will somepony be able to give him the happiness he deserves and save him from a prophecy that ends with his death?

Across Equestria and through Earth, two hearts will join together, but one may die to ensure the survival of reality...

Cover image drawn by jmkplover and colored by Saljian

Official Theme Song done by XAVI- Playful Banter

It even has a Tvtropes page!

Spiders and Magic: Rise of Spider-Mane