Based off of this Comic from doubleWbrothers
The beginning of the Daughter Starlight Timeline

Starlight Glimmer caused some troubling problems with Twilight and her friends. What past caused this pony to go down such a path? How did Twilight fix such a horrible past to make this pony better?

Check out the sequel

Bonbon has been trying to get to know Lyra for years, but the unicorn refuses to show her true self or accept Bonbon's advances. When Bonbon discovers that Lyra is leaving town without even saying goodbye, Bonbon decides to follow, no matter how far they must go or how hard Lyra protests. Rainbow Dash tags along as a guide, paid by Lyra for her services, but the tight-lipped Wonderbolt appears to have her own motivations as well.

It's all secrets and lies, but Bonbon is determined to get to the truth, even if it takes her to the end of the world. And it just might.

- Big thanks to Thanqol for his aid in prereading and reviewing
- Featured on Equestria Daily
- Interview about this story

The unstoppable farce is moving on Canterlot. Tales were told of the evils done by Nightmare Moon, yet history had forgotten those perpetrated by the Minions of Nightmare Moon. Soon Celestia's worst nightmare shall rise again and the two things they want most, are two things that the Princess refuses to give up.

Trigger Warnings: Fart Gun, Senseless Mayhem, Sororicide, Happy Ending?

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.

Imagine being stuck in the mind of a pony that you can't stand and is the exact opposite of you.
Now imagine having your life torn away from you, and you've just gotten it back; only to face just as many hardships as before.
And then imagine you were just told you technically shouldn't even exist.
That's my life.

This story is a sequel to Caged Inside, but is written in a way that it's not necessary to read it first.

Traveling between parallel universes is impossible, especially during the process of regeneration, but the Tenth Doctor doesn't have time to question the facts. He's just been thrust through a tear in the fabric of reality, gotten a new body, and landed on a planet called Equestria. Specifically, he's landed in the worst possible place in all Equestria – somewhere that's ready to unleash a “big ol' storm of chaos”.

That's just the beginning of the Doctor's strange new lease on life: there's a whole host of mysteries to explore. Who is Derpy Hooves, the gray pegasus who understands more about him than even she knows how to explain? How does Princess Celestia already know him? And what's the truth behind the Order?

Above all, the Doctor needs to discover if this new universe can heal the wounds he suffered in the last. Only one thing is certain: there's an awful lot of running left to do.

(Warning: For those of you who haven't watched up to the Doctor Who episode 'The End of Time'... spoilers. Also, this story begins between Seasons 2 and 3 of FiM, and things start to... diverge from there.)

Side stories can be found at The Merely Mundane Tales (of a Mad-Pony in a Box).

Only a few hours after she learned of the Griffon Empire's invasion, Princess Celestia surrendered herself to the griffon army and asked for an audience with the Griffon Emperor.

The Emperor thinks she's here to negotiate Equestria's surrender.

He's wrong.

Spanish Translation
Polish Translation

As the eternal regent of Equestria, Princess Celestia's knowledge of magic is without equal. Over her long life, only a few gifted ponies who had a great destiny before them have had the honor of learning at her side. Sunset Shimmer was one such pony: one of Celestia’s best and most promising students. As she learned at Celestia’s hooves, their bond strengthened until they became far more than student and teacher to one another.

Sometimes those closest to us are the ones who can hurt us the most.

[Note: This story does not directly tie into Equestria Girls]

This story is a sequel to An Empress' Wish.

Chains and bars are what hold a prisoner from escaping physically. Mentality and reflection are what holds a prisoner from escaping emotionally. Once a prisoner to chains, whether of mind or body, you are a prisoner by all names.

The only consolation of being imprisoned is that you are alone with your thoughts. Thoughts of what went wrong and how you found yourself where you are.

As a filly, Sunset Shimmer made a difficult choice which affected not only the rest of her life, but the course of two worlds, when she turned her back on her mentor, her promises, and Equestria itself.

But there's more than one of everything, even entire worlds.
Now, another Sunset Shimmer, living in another world, comes to that same decision of trust or betrayal.

Though there are many Sunsets amidst creation, do they all share one fate?

Edited by Prak
Prereaders: Foals Errand and Minifig
Special Thanks to Between Lines
Art used with permission by SilFoe