This story is a sequel to Better Living Through Science and Ponies

THIS STORY IS CURRENTLY BEING REWRITTEN. PLEASE READ:
I've decided to rewrite this entire story. Considering that I began this project with almost no creative writing experience, I was bound to make some pretty bad mistakes. The story flow is not well organized, and there is an unhealthy amount of redundancy and poor pacing, as well as some pretty important things that I should have included. I intend to address these issues to the best of my ability, but it will be a long and arduous task. This story means a lot to me, so I want it to be more than the mere amateur mediocrity that it resembles. So, give it a read if you want, but keep in mind that it will change. I recommend that you put this on your read later list in the meantime.

This is a Portal 2 crossover. If you haven't played Portal 2, please do that first. Then read the prequel if you haven't done that either.

After Chell finally escaped the confines of Aperture Science, a freak portal mishap down below transported her, along with the entire Enrichment Center, to the land of Equestria. Upon entering this world, she was transformed into a pony. In a strange body and in a strange land, Chell was fortunate enough to be accepted by the ponies of Ponyville, and she lived out a new life contently among the ponies.

But that peace was not to last, for GLaDOS took a particular interest in the ponies of Equestria, and after two weeks of preparation, she launched a surprise attack and kidnapped 300 ponies to serve as test subjects, including Chell's friends and the princesses themselves. Once GLaDOS had them, she subjected them psychological torture. To save her friends, Chell made her way into the one place she hoped never to see again. In doing so, she freed the ponies, defeated GLaDOS in battle, and helped bring about the destruction of the facility. Although this made Chell a hero, she paid a terrible price in that brutal fight.

Beaten, battered, and traumatized, Chell spent months recovering from her wounds. After returning home from the hospital, all she wants is to once again live a normal life in Ponyville, but to do that, she must first heal from her wounds, both physical and psychological.

At the same time, GLaDOS herself has survived Aperture's destruction. With nothing left but herself, she vows to get back to testing. Though she faces an uphill climb, she is determined to see her facility rebuilt and the testing resume, and will stop at nothing to achieve this.

Has a TV Tropes page (will need to be updated after rewrite)

The works that this fanfiction is based on are properties of Hasbro and Valve. I would like to thank Pen Stroke for writing the original story and Flyer for his assistance and advice.

Please note, this is an unofficial sequel. I have received permission from Pen Stroke, but it is not canon to the original. I hope you enjoy it, but keep in mind that this is a fan work (of a fan work), and Pen Stroke holds the rights to the original story.

This story is a sequel to Fluttershy's Second Greatest Secret

Scootaloo somehow managed to get an interview with the Ponyville most well known musicians for the Cutie Mark Crusaders. The musicians were Octavia and Vinyl Scratch, during the interview Octavia was skeptical about of her best friend, she didn't have much to say and she was acting odd around them, and then she realized that she doesn't know much about her herself. So after a while Octavia's curiosity gets the best of her and is determent to find out why that is. Finding out Vinyl's Jarring, embarrassing and interesting secret in the process, along with a filly named Sweetie Belle.

Comedy is debatable.
And so is Slice of Life.

Read in either of these orders you like. But as of now they barely connect.
Chronological order:
Fluttershy's Second Greatest Secret
The Club's Connected to the Boutique
Well, That's Just Silly

Chronologically made:
The Club's Connected to the Boutique
Fluttershy's Second Greatest Secret
Well, That's Just Silly

In a moment of weakness, Chrysalis had more than a taste of Shining Armour's love. 11 months later, Twilight Sparkle finds herself a brand new niece by way of 'A small foal in a basket on my door step'.

Special thanks for the picture by Awilldrawforfood1
Now edited with DoomManta.

After an accident, Rarity and Twilight are thrown in a race against time to stop their transformation into changelings before they become part of Chrysalis' swarm forever.

On secret assignment from Princess Celestia herself, Twilight investigates a powerful magical artifact for clues to the mystery of Luna's transformation in the evil Nightmare Moon. Incautious use of the artifact sends Twilight hurtling back in time. Can Twilight discover what caused Luna's transformation? And will she ever make it home again?

Kickass cover art used with permission from Bitz.
http://allthebitz.tumblr.com/

It was just a normal day for Twilight Sparkle, and that's when she found an old book, a relic of Starswirl the Bearded. That's when it happened, that's when she became a Master, how Starswirl the Beared became her Servant, and why she must now engaged in a to-the-death battle royale against six other Master and Servant pairs – all in the name of some holy artifact with an incomprehensible power that must not fall into the wrong hooves.
A My Little Pony and Fate/Stay Night crossover, written to be comprehensible to those without any experience with Fate/Stay Night.

Authors: Stalin the stallion, Crushric
All art by Stalin The Stallion
Huge thanks to The Conflicted Writer

Collab with y1

When Luna reappeared on Nightmare Night, she was no longer the small filly from before. Now an adult mare, she commanded the same respect and presence as that of her sister, Celestia. Many assumed that this was the result of her powers coming back to her naturally, but that was a lie happily perpetrated by both Celestia and the Gryphon Kingdom.

This is the story of Luna as she struggles with the remnants of Nightmare Moon and her forgotten past. The only clue she has is The Temple of the Stars where her small group of worshipers used to gather, which now lies in ruins and in the clutches of the gryphons. Some things were forgotten for a reason and the past always has a way of returning.

These two facts are well known by Gilda. Pulled along for the ride against her will, ghosts of a forgotten past have come crawling back, intent on dragging her back down to a fate worse than death. All the while, she seeks to preserve the innocence of those untouched by war and tries to protect Trixie from the harsh truth beyond Equestria's borders.

One wrong step and war shall erupt. One wrong step and the world will be plunged into a darkness that would rival Discord.

Hope is not a plan.

This story is a sequel to Elementals of Harmony

Ditzy Doo returns home one day to find an old friend waiting for her with dire news and a brain in a jar. With the latter, she will witness the answer to a pair of ominous questions: What if Jin-Gitaxias was a brony? What if New Phyrexia tried to invade Equestria?

As noted above, this is a sequel. Read the first story first, or little if anything will make sense. A certain level of gore and body horror will inevitably arise, given the nature of Phyrexia (For the card game illiterate: Like the Borg, but with more magic and much less attachment to the humanoid form.)

Cancelled after a long remission. You can see what would have been here.

It has been 300 years since Celestia vanished through the efforts of cultist separatists, and Twilight Sparkle formed the Wardens of Harmony to force the Everfree Forest to spread in order to balance out the world, as well as defeating the monstrous Nightspawn that came from the darkness.

In the walled city of Canterlot, Comet Strike is a unicorn trapped by circumstance, spending day after day living in a bubble of tedious classes and strict rules. All this changes when Comet discovers plans for an attack on Canterlot and helps to foil it. Nightspawn, thought to be wiped out, resurface. Set on a dangerous adventure, Comet and her friends must build alliances and keep friendships to find the Elements of Harmony and save Equestria from the eternal night and a treacherous foe.

(Crossover is a loose world and concept merger with that of the Dragon Age video games. Teen rating is for mild violence and very mild gore. )

The criminal organization known as akatsuki have completed their long acomplished goal of capturing the nine tailed beasts, already sealing the first seven. When attemping to seal the final two, however, something goes wrong, and the group is sent off their planet.

Waking up, they discover they have been transformed into colorful horses, yet they still posess there ninja abilities. Now travelling through the land, they begin a quest to find a way to return to their world. They are determined to get back, no matter who or what stands in their way.

This story depicts an alternate universe where the members of the akatsuki were not killed. Continuity and other factors from the origional timeline will be altered
For entertainment purposes.

Alternate Cover art

Special thanks to Thardoc for editing for me