After discovering that Cadence is not who she appears to be, Twilight is sent to another world entirely by the disguised Changeling Queen to avoid her plan being disrupted.
When Twilight lands, she discovers that not only have Spike, Owlowiscious and Peewee followed her, but that they've arrived in a world where the main sentient species is human.
There's still a place where they teach magic, though.
Crossover with Harry Potter. Twilight will be effectively taking the role of Hermione.

I've marked this story as cancelled to reflect the unlikelihood of it continuing. If I do come back to it I'll revert that.

It has been two years since the events of Yu-Gi-Oh! 5D's. The Fortune program had been successfully installed into the Momentum Network, ensuring that it would never go out of control again and it seems that all is at last right with the world.

But when Yusei hears the voices of his Equestrian friends crying out through an anomaly in Satellite, Yusei revs up his D-Wheel once more! An old foe has returned to finish his mission once and for all, and it's up to Yusei to stop him! Can Yusei find and stop the sinister Paradox before his time-jumping destroys Equestria and his future?

This wasn't supposed to happen, but I said that I could come up with a sequel if I wanted to and my brain mistook that for an order. This story was born as a result. So hang on tight, my bronies! This is gonna be one hay of a ride!

DISCLAIMER: My Little Pony! Friendship is Magic, all Yu-Gi-Oh! characters, and the Yu-Gi-Oh! Trading Card Game are copyright their respective owners. All original story elements, including original cards, their names, and their effects, are mine and may not be reproduced without my consent.

Remember the time Ponyville was invaded by Parasprites? Or the time Cerberus, the demonic three-headed dog guardian of Tartarus, Equestria's underworld, wandered away and ended up in Ponyville?

What I'm trying to say is, it's an odd sort of town. Anything can happen.

This is the story of how a million star spiders came to live with Twilight Sparkle. It wasn't even the weirdest thing to happen to her that month.

Ponyville, man. Crazy place.

Edit: Now a reading, apparently!

After saving the future from Paradox, Yusei prepares to return to his own time. But when the Crimson Dragon veers off course in the rift, Yusei finds himself in a strange new world... populated by brightly colored talking equines. Yusei meets Twilight Sparkle and her friends and becomes their friend as well, even teaching them how to duel. But something isn't sitting right with Yusei and he soon learns why he was brought here when an ancient enemy reappears and goes on a destructive rampage.

This is my first attempt at pony fanfiction, though not my first try at writing in general. I have no idea how this is gonna go, but be honest.

Regarding the duels: I intend to describe the actual gameplay just as much as the monsters and card animations. I'm not just a fan of the Yu-Gi-Oh! franchise, but a Duelist myself. As far as the rules go, I'll try to help the unfamiliar understand the game in the beginning. Card and player stats will also be displayed during the duel portions of the story (I'll try and write it so that they don't disrupt the flow of the story too much). But beyond the stats and character descriptions of their cards, you'll have to look stuff up yourself. You can do so on the Yu-Gi-Oh! Wiki.

DISCLAIMER: My Little Pony! Friendship is Magic, all Yu-Gi-Oh! characters, and the Yu-Gi-Oh! Trading Card Game are copyright their respective owners. All original story elements are mine and may not be reproduced without my consent.

The Mane Six, Spike, and the two alicorn princesses are sucked into an alien world. They soon discover that they have been transported to a galaxy far, far from home. A galaxy which is under the control of the evil Galactic Empire and where Emperor Palpatine knows of them and wants to use them for his own nefarious purposes.

Twilight must lead her friends on their journey through a cruel and hostile galaxy, avoiding the Imperial forces and bounty hunters sent after them, trying to find the Rebel Alliance.

They may be the ponies' only hope for getting home . . . .

Bonus: here's the main title music for this story https://www.youtube.com/watch?v=QB4xZpWumYg

After fighting off the alien fleet that menaced Earth, XCOM turns their focus to warning other worlds of the possible threat. When Doctor Moira Vahlen is accidentally sent to one of those worlds, she learns that the the invaders have attacked Equestria. Who will protect them from the horrors they're about to face?

Sorry, I should clarify that last bit. Who will protect the aliens from what they've just gotten themselves into?

Neo Domino City is a war zone. The mysterious Black King has spread his shadowy influence throughout the once-thriving metropolis. A small resistance movement is fighting against him, but they can't last much longer without help.

In Equestria, the balance is beginning to shift to the darkness. Twilight Sparkle and her friends are sent across dimensions to the human realm to discover the source of the imbalance and to repair it. But she'll discover much more than that, and will eventually learn the true connection between her universe and Yusei's.

DISCLAIMER: My Little Pony! Friendship is Magic, all Yu-Gi-Oh! characters, and the Yu-Gi-Oh! Trading Card Game are copyright their respective owners. All original story elements, including original cards, their names, and their effects, are mine and may not be reproduced without my consent.

A pariah who has long lived in their elder sibling's shadow, only to try and violently assert their own greatness and fail...both Loki and Luna know this tale all too well.
After the events of Thor, Loki Odinson of Asgard has fallen from grace, only to find himself in an unknown realm. Reaching out to him is Princess Luna, whom finds the similarities between them. Will Loki accept her help and recover from his dismay, or will he end up spurning it because of his arrogance?

More info below the break.

Arc 1: Entering Equestria 1-13
Arc 2: The Avengers 14-23
Arc 3: The Great and Powerful Student 24-33
Arc 4: Delving into Hel Itself 34-46
Mini Arc 1: Lorelei the Temptress 47-48
Mini Arc 2: The Equestria Games 49-50
Arc 5: Thor The Dark World 51-57
Arc 6: Calm Before the Storm 58-70
Arc 7: The Performance of a Lifetime, the Fall of Thanos 71-75
Arc 8: To Remember When One Should Forget 76-80, Epilogue
Bonus Chapters

Cover image from CuteSkitty on Deviantart: http://fav.me/d5whxcz

When a mysterious ship appears in Equestria, the Cutie Mark Crusaders take the opportunity to get their cutie marks in sailing. Unfortunately, said ship belongs to the Outworld Emperor Shao Kahn, and is collecting combatants for the latest Mortal Kombat tournament. Now, Twilight Sparkle and her friends are forced to enter the tournament to save their friends and stop Kahn from taking over the world.

Crossover fic based loosely on the 1995 MK movie. Violence tends towards the comedic variety rather than hardcore blood and gore.

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.