A Metroid crossover.

After destroying the X, the Galactic Federation charges Samus with treason and hunts her down. While running from the Federation, Samus manages to escape but ends up crashing in Equestria, far from any explored sector in the universe and with no way of returning home. Can the most feared bounty hunter in the galaxy adapt to a land full of talking, magical ponies who think friendship is magic?

Some notes:

1. This takes place after Metroid Fusion, which is the last game in the Metroid chronology/timeline so far. It also takes place after season 2 of My Little Pony: Friendship is Magic.

2. Samus crash lands on Equestria and meets the mane 6. I'll try to not make it too cliche. Also, no ponified Samus (at least, not planning to).

3. In this story, Samus is a Federation runaway. They are hunting her because she destroyed the X parasites in Fusion and they wanted to research on them (I recommend checking the Metroid Wikia for reference).

4. I'll take the 'Tragic' as not so tragic. Don't expect deep depression from this story.

5. I'm open to ideas! Any review/comment is greatly appreciated. Feeding my ego will increase the chances for updates!

6. Any story inspired or ripped off from this story WILL catch my attention. Please tell me if you are going to write one, so I can read it!

Without further ado, enjoy!

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Original artwork by johnjoseco. DA page
All I did was paste Samus.

After the defeat of Queen Chrysalis, the changelings left behind don't know what to do. They eventually decide to seek the one who defeated their queen and make her theirs. What really goes on in a changeling's head? Can Cadence handle the vile creatures without prejudice? What do the crystal ponies think?

Teen due to cursing, only references to sexual stuff, and cursing

Long ago in the beautiful kingdom of love and prosperity, a queen ruled over the kingdom.
Her fur of white,
Her mane of teal,
and her crown of gold.
The subjects loved her dearly, until the night of the ball.
Then she was kidnapped.

If you want this story, P.M. me; I'm done with this.

Meet, Fragment. A changeling with amnesia. With his memory loss adventure ending before it could begin he is brought before Princess Celestia who takes this lost changeling under her own wing in a hope to mend the two species' relations, but many trials will be had which will strain this changeling's trust between the hive he knows nothing about or the ponies that sheltered him. Fragment's past will pursue him as flashbacks slowly show him what his life used to be...

Cover art by sicher999! (dA page here!)

Thanks to Out of Place for helping with the description.

This story is a sequel to A Stitch in Time

Having discovered the message left for her by Star Swirl the Bearded in the distant past, Twilight once again finds herself caught up in the middle of a struggle against forces far greater than herself. In order to even stand a chance she'll need to travel further and wider than she ever has, and forge some unlikely alliances with old enemies. All to bring down the powers that have manipulated and shaped her entire life, and retake control of her own future.

The conclusion of the Time Loop Trilogy, which began with Hard Reset
Available in Spanish thanks to dgs1993
Series TV Tropes page

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page

Twilight Sparkle finds herself inside a cocoon in the throne room of Canterlot Palace along with her friends and many other ponies. She is thrust into a dream world by Chrysalis who is feeding on the feelings of love and friendship she and the others will experience in their alternate realities. In her dream, she finds Princess Celestia, who has been able to cross between dream worlds. Twilight and Celestia must now travel between dreams in order to awaken their friends and stop Chrysalis. However, some dreams are not as happy as they expected, and some secrets held in the subconscious may be better left unawoken.

Additional character tags: OC's, Princess Cadence, Shining Armor, Princess Luna, Nightmare Moon, Trixie, Zecora, Diamond Tiara, Snips, Flitter, Cloudchaser, Roseluck, Big Macintosh

Inspired by the fan video of an alternative ending of season 2. Click here to watch it!

Featured on Equestria Daily 9/14/2012.

Now a comic illustrated by Zoarvek! http://zoarvek.deviantart.com/gallery/48143295

"Sex" tag added on 10/12/2014 due to sexual themes here and there. It's not the focus of the story, but it's in there. For a more detailed explanation of why the tag was finally added, see the author's note on "Corruption Ch 10"

Old cover art here: http://i.imgur.com/Tgt974q.jpg
Full size: http://i.imgur.com/9uWAX.jpg

When Twilight Sparkle slipped beneath the covers last night, everything had been fine. She had friends whom she loved, a teacher she adored, and a bright future ahead of her. But when she woke up, her blankets and quilts had been replaced by hospital gowns and padded restraints.

Everything is wrong and nothing makes sense; even her friends have changed. The doctors keep telling her that she is sick, that none of it was real and that it was all in her head. Yet she remembers a life far beyond the hospital walls. She couldn't have made it all up on her own. They must be lying… right?

Ask Asylum Twilight - Still updating regularly!
Equestria Daily
TVTropes
Asylum Fan Group
The Tartarus Project
Russian Translation
The Asylum 20,000 View Spectacular Stage Show!

Art:
Asylum Cover by conicer
Twilight and Twilight Smiles by dreamingnoctis
Mirror Twilight and Plague Doctor by Jaestring / BloodGoldWings
Twilight Smiles and Doctor AJ by conicer
Nurse Ratchet and Silas and What's in the mirror? by Archonix
Doctor AJ Sketch by Archonix | Colored and vectored version by ReFro82
Twilight's Asylum by Khan the Cake Lover
Smilight by HappySwitch
Twilight Waking Up by Dombrus
Fan Art by toxicdemon10
Asylum Twilight by Madness-With-Reason
Asylum Fluttershy and Asylum Ch 26 by Downburst-Backspace
Twilight and her Twin by v747
Birdgirl by sirValter

Readings and Videos:
Asylum Animated Trailer Video by formuladash
Reading by Gammarobot (SugarCubeRadio): All Chapters Here
Reading by Ender Brony: All Chapters Here
Reading by VisualPony: All Chapters Here
Reading by MelancholyIguana: All Chapters Here
Fan Trailer by Kaidan: Asylum FanFic Trailer Cuckoo's Nest

Sanctuary by Kaidan
Broadhoof Files: Dr. Humors by TypewriterError
Broadhoof Files: Corporal Phalanx Spear (Ret.) by Phalanx Spear
A Hearth's Warming Tragedy by Seven Fates

A special thanks to Breath of Plagues, Rex Ivan,
ChudoJogurt, Cynewulf, Death the Kid, Selbi, PrinceDolph, Blahman2816, Queue, and Gage!

Axan Zenith - Dr. Dreamer
Dratini4 - Way Finder
psychicscubadiver - Bright Mind
Velkaden - Dream Chaser
Reese - Silver Glow
Viola Heartstrings - Clover
Archonix - Spinney Whiteacre