Okay, so I kind of failed with my first attempt at writing a Xenoblade/MLP crossover, so I then decided to take it from a different angle: bringing all the inhabitants of Equestria into the world in Xenoblade, with the MLP timeline being post Season 4 and prior to the events of Xenoblade.

After interacting with a plot device, Twilight Sparkle finds herself in the outskirts of Colony 9, at the same time when Shulk and Reyn are looking through Junk. After a brief misunderstanding, Shulk and Reyn invite Twilight Sparkle with them, the three of them journeying back into the Colony.

At the Defense Force Fortress, Applejack wakes up and sees a group of soldier homs, curious as to what she was. She goes on the defensive, questioning the group around her with hostility. Luckily for everyone, Shulk, Reyn and Twilight Sparkle arrive into the fortress just in time before things would get ugly. After a few introductions and stuff, Twilight Sparkle realizes that more of her friends are scattered throughout the Bionis.

Rainbow Dash awakens within the Refugee Camp within Gaur Plains, where she interacts with all of the refugees from Colony 6.

Spike awakens within the Satorl Marsh and noticed just how dangerous it is. He's in hiding until the party finds him.

Fluttershy awakens within the Frontier Village, the ancestral home of the Nopon. She would be first seen babysitting Riki's children.

Rarity awakens in Alcamoth, where she interacts with the High Entia and learns from them, teaming up with Melia on her mission.

Pinkie Pie awakens within the Machina Village on the Fallen Arm, where she was greeted into the lifestyle of the Machina. She also helps out the beings that fall onto the Fallen Arm from the Bionis, using her Pinkie Senses to locate them.

The characters from the show would be spread across the civilizations and such, but they would play no direct role. Some events from Xenoblade Chronicles' story would also be changed due to the intervention of ponies. I would appreciate any feedback on the idea in order to improve upon it.

So I began writing it, and my idea for weapons so far:

Twilight will use the ring that she got before Equestria collapsed actually a Monado
Applejack would either use a hammer, ball and chain or something akin to brass knuckles for ponies.
Rainbow Dash would use ????
Spike would use claws
Rarity would use an ether orbitar
Fluttershy would use a woodwind instrument
Pinkie Pie would use dual guns

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Sorry I'm so late to this party. This looks like a really good idea! I love Xenoblade, despite getting stuck at the Spider-Mechon Queen so early. (I do know about half the story.) I look forward to reading this story!
Also, mayhaps Rainbow Dash uses twin swords? Flying around with them as she slices past the enemy.

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I would have done that, but that's Fiora's sub-class of weapons.

3592853 Ah. That's right. I always thought of them as knives, but I suppose you're right.
There isn't anyone using a bow and arrows, right? Oh, wait. In a world with guns, that's sort of dumb.
Well, anyway, Good luck! Not that you need it!

3575718 Did you know? The man who voiced Miqol of the Machina, was the same man who voiced Daddy Pig in Peppa Pig.

Your childhood is ruined. You're welcome.