This story is a sequel to Sweet Apple Anthology

Far in the West, out in the frontier, Babs Seed and Apple Bloom have found an adventurous, satisfying life. Business at their bar is booming and supporting Sweet Apple Acres, ending Applejack's economic woes (for the time being). Babs has reunited with her father and the savior of her foalhood, Turner. North of no-pony's land, Citrus, Libra, and Braeburn are thriving in Appleloosa, though tensions between the locals and an influx of emigrants threaten to shatter peace in the tiny town.

Far in the East, in the belly of the beast, the once-glorious city of Manehatten has collapsed into a haze of unimaginable chaos and depravity at the hooves of its King. A King whose chessboard is rapidly expanding and whose Knights march to conquer and annex in the name of their Master.

When East and West clash at last, who will be left standing?

Third installment in the alternate universe timeline started by Tangled Roots. Preceded by Sweet Apple Anthology and beginning from the first story's Epilogue.

Coverart by the awesome artist Lulubell.

Now with a TVTropes page! Thanks to vren55 for putting it up!

Rated Teen for strong violence, language, and darker elements. Sex tag is for implied sexual situations.

A long, long time ago, the necromancer Grogar conquered the city of Tambelon for his own nefarious purposes. Working together, the princesses Celestia and Luna were able to banish Grogar and the fallen city into the realm of Shadow, never to be seen again...or so they thought.

Two thousand years later, Tambelon and Grogar return - and the world may never be the same...

A Lunaverse story, and the premier of Season 2!

Corona Rises!

Octavia wanted to forget war. She wanted to live a normal life not filled with bloodshed, and focus on her music career. Unfortunately, war is rarely considerate, so when the changelings invade, Octavia has no choice but to act in order to save her country from possibly a threat worse than even the War of 1972.

But in a city taken over by creatures that can take any shape, who can you trust?

This story is NOT a retelling of Metal Gear Solid, but it uses some of the tropes from that game.

This story is a sequel to Boast Busted

Scholar … Prodigy … Fugitive …

After an unfortunate turn of events, Twilight Sparkle has found her self on the wrong side of the law and on the run. It wasn't her fault though, well maybe a little, but Trixie was the real criminal. That witch, she had tricked Twilight into all it! If only there was some way to prove to Princess Luna who the real Element of Magic should be.

If only there was some way…

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-- This story is set in RainbowDoubleDash's Lunaverse, and is a sequel to the events of Boast Busted. If you haven't already read that fic you should consider doing so for improved context.
-- Twilight Sparkle vector by Klarnetist

Space will leave you breathless, and so will many other things within it. But there are things being hidden from us. Things that, if found out, could ruin a thousand lives... but they could save a million more.
So the question is: would I want be the one to discover them?

'MLP:FIM' is owned by Hasbro
'X-Com Enemy Unknown' was developed by Firaxis Games and published by 2K Games.
'X-Com' was originally developed by Mythos Games and MicroProse

Twilight Sparkle is lost and broken, living a new life in a new town, she has forgotten who she truly is. Something happened to Twilight in Equestria that caused her sudden departure, and has half of Equestria scouring the planet for her.
"What did I do?" Is... not a question Twilight had thought of. She'd been happy, and content living her new life in Frostglade. However, she'd always felt like there were pieces to herself missing. Like, she'd lost something important.

When Sunset Shimmer and Trixie Lulamoon finally track her down after months of searching (and barely tolerating the other's presence), the reunion is not a happy one. Their presence has upset Twilight's new life by revealing the first step in unraveling the web of secrets bottled up in Twilight's psyche.

The three mares journey to a place of ancient magic, where they must piece together Twilight's shattered memories, solve the mystery, and then finally go home to where they truly belong. Of course, their journey will not be easy; dark shadows follow Twilight's every move, trying to stop her party from seeing the truth. If that weren't bad enough, it's not just Twilight Sparkle who is being tested by the challenges of the Nexus.

Tragedy strikes.
A nation affected.
Old, the young, rich or poor, all alike to the touch of sorrow and fear.
All are affected.
All have stories to tell...

The various side stories of The Secret Life of Rarity. If you think of a good story for this universe, please send it to me and I shall include it!

A Metroid Crossover

A meteor, resistant to magical manipulation, crashes in Equestria, Planet Equis, and soon spreads an unknown poison throughout the land. Containment is all but failing and the Princesses have little power to stop the spread of the Great Poison. The Elements of Harmony are of little use as no knowledge exists of this threat that consumes all life. Help comes from a certain Hunter, clad in metal.

Samus Aran will not only fight for her life as always, but her own sanity as well as these ponies that she begrudgingly starts seeing as allies. New horrors and abilities await her as a reason to fight slowly festers within her, possibly unlocking something she had been denied for so long: Friendship.

Notes and Resources:

This takes place after Echoes. The events of Corruption will have not happened yet. In terms of MLP, consider everything up to and including the Crystal Empire. Princess Twilight does not exist here, etc. The official Metroid Timeline can be found here.

As well, this story references the manga in many places. Reading of it is not required and I try my best to explain the context, but if you're interested, both volumes can be found here.

EDIT: This story was written over two and a half years, beginning in 2013. You'll probably notice the difference in writing as the chapters progress.

The story is generally the same. A group of ponies go on a quest to stop an insane alicorn who had escaped banishment, learning about friendship along the way and mastering the Elements of Harmony. But the details...

It can be Trixie Lulamoon leading the Elements of Harmony against Corona.
Rainbow Dash could be Celestia's student and go to Ponyville.
Equestria could have a deep connection to three young people in its distant past.
The Elements of Harmony could have been moved to Manehattan for the ponies to quest for.
Princess Cadance might rule over an Equestria of music, with Octavia as her prized protege.
Or Spike and Twilight might have their roles reversed, the former a stallion and the Element of Magic.

And each one has been chosen by Discord, an Element removed to a seventh Equestria for purposes as yet unknown. Can they survive? Can they get home? Read and find out!

The Lunaverse was created by RainbowDoubleDash and is used with permission. Opening segment was written by Talon and Thorn.
The Hasbroverse was created by RK_Striker_JK_5 and is used with permission.
The Manehattanverse was created by Little Jackie Papercut and used with permission.
The Cadanceverse was created by GrassAndClouds2 and used with permission.
The Flipverse was created by Bed Head and used with permission.
The Dashverse was created by Trinary and used with permission.

And special thanks to dramatic_spoon for getting this all together.