There is a secret in Equestria. A secret the newly crowned Princess Twilight Sparkle doesn’t dare to believe. Like puppeteers pulling on marionettes, they have influenced Equestria for better and worse since the fall of Discord. So far they have been benevolent, but their potential for evil is vast. What’s worse, she doesn’t know their name. She doesn’t know their mission. All she knows for certain is one thing.

That they all seem to be zebra.

After a mishap with a spell lands Twilight Sparkle and friends in the village of Konoha, Tsunade and Jiraiya turn the accident into a plan to shield Naruto from Akatsuki...whether he knows it or not. Now living in Ponyville, Naruto must adjust to being a pony, but with his assistant and the Mane 6 to keep him company, that might be easier than he thinks. Crossover with Naruto. Originally posted on Fanfiction.net

After a long day of flight practice with Scootaloo, Rainbow Dash discovers the filly knows next to nothing about preening and takes it upon herself to teach her.

Warning: May Contain Feels and/or D'aww moments.

Featured on FIMFiction on 7/20/2013. Yay!
Featured on EQDaily on 09/12/2013 Double Yay!
Reading by TheLostNarrator (excellent!): Here
Reading by DRWolf: Here
Reading by Joehighlord: Here
Riffed by Draklox: Here
Korean Translation: Here
Spanish Translation: Here
French Translation: Here
Chinese Translation: Here

With some changes on Star Swirl's time spell, Twilight accidentaly gets trapped in the past. But after saving two fillies and enlisting them to be her students in magic, they go on adventures together to survive the ruthless world they live in. With new friendship and foes, they discover what it truly means to be family by choice.

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Now with the collaborative efforts of Angel Bunny, Fausticorn and soulwinds!
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Art by awsdemlp.deviantart.com
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People who I am in deep gratitude for offering help:
amacita
MidnightDancer
Skunktrain
Cerulean Starlight
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And FAN ART by 1110soulite!

In the wake of the massacre of the Uchiha clan, a mysterious masked man steals a bargaining chip and the Jinchuuriki of the Kyuubi in one fell swoop, locking them away in the realm of Kamui. Uchiha Sasuke and Uzumaki Naruto join forces to find their way out, yet what they escape to is not their home, but another world altogether. Turning their backs on their hardship and pain, Naruto and Sasuke embrace this world with open arms.

But what if their presence were to interfere with a scheme one thousand years in the making?

This isn't entirely my work. This story was started by kiddi. He wrote the first 4 chapters. He feels he can't continue and has given me permission to continue it.
Naruto Uzumaki is lost to Konoha when he vanishes durring an attack on his life. He winds up in the magical land of Equestria in under the care of a certain Zebra. But this is only the beggining as much larger things are in story for are young traveler. Watch as he grows and faces numerous challenges caused by his past and his future.

The fourth great ninja war was over. With Sasuke's help, Naruto vanquished Madara and defeated the Juubi. However, when all was said and done, the two were betrayed by those they trusted most. Fearing the outcome of the toad elder's prophecy, The survivng kages threw Naruto and Sasuke into time and space with the hopes of banishing the two forever. The two however, manage to end up in an entirely new world, giving the two a possible fresh start. Their arrival however, changes the outcome of upcoming events in this world in ways that should never have happened.

It was an ordinary day in Equestria. The sun was shining, the birds were singing and princess Celestia had some free time from her royal duties. Then the explosions started, explosions originating from the Everfree Forest.

Cover art supplied by RainbowDashVegetaFan123

A ninja and a DJ.
A human trained to eliminate his enemies, and a pony skilled in destroying one's hearing.
Both of them have an... interesting fashion sense.

It's like they were made for each other, isn't it?

Rated for mention of naughty bits.

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.

Weird and unique creatures (Pokemon) start appearing all over Equestria, from Ponyville to Canterlot. The creatures seem friendly though.
Could the appearance of these creatures have something to do with the odd comet that popped up in the sky one night?

Note:I will add more character tags as the story progresses.
double note: thank you the myth for editing this, wuv you lots bro!
triple note: the story takes place before season 3.