A Metroid Crossover

A meteor, resistant to magical manipulation, crashes in Equestria, Planet Equis, and soon spreads an unknown poison throughout the land. Containment is all but failing and the Princesses have little power to stop the spread of the Great Poison. The Elements of Harmony are of little use as no knowledge exists of this threat that consumes all life. Help comes from a certain Hunter, clad in metal.

Samus Aran will not only fight for her life as always, but her own sanity as well as these ponies that she begrudgingly starts seeing as allies. New horrors and abilities await her as a reason to fight slowly festers within her, possibly unlocking something she had been denied for so long: Friendship.

Notes and Resources:

This takes place after Echoes. The events of Corruption will have not happened yet. In terms of MLP, consider everything up to and including the Crystal Empire. Princess Twilight does not exist here, etc. The official Metroid Timeline can be found here.

As well, this story references the manga in many places. Reading of it is not required and I try my best to explain the context, but if you're interested, both volumes can be found here.

EDIT: This story was written over two and a half years, beginning in 2013. You'll probably notice the difference in writing as the chapters progress.

Warning; This is not to be taken seriously, and the degree by which humans win (spoilers) has been amplified for the purpose of comedy.
Have you been reading a 'Human/Pony War' fic and been wondering how the ponies are putting up a fight with medieval level weapons and magic, while we have firearms, nuclear weapons, armies the size of their entire population and most importantly, years and years of perfecting the art of war. This is how an actual human/pony war would go.... with comedy.
9/11/14- FUGGIN A, I GOT FEATURED! Holy crap I go to sleep after sending it for submission, wake up, check it, pretty good support, I go to school, come back and I have hundreds of comments, favorites and 10 new people followed me
10/11/14- Christ, we're 3 likes away from 1,000.

UPDATE: COMPLETE! You may have heard of Pipsqueak. He's a pinto colt, originally from Trottingham, saved Nightmare Night from being abolished seven odd years ago. Know the one I'm talking about? Yes? Good. Since then he's grown into a charming, cultured hedonist who wants to bed near every mare in Ponyville and a good few of the stallions. He has a slender build and some ponies say he has mares' hips, though he feels that those ponies should shut their bloody mouths. His best mate is the gregarious and multi-talented Featherweight, and his other best mate is the stoic trencherpony and excellent cook Chowder.

This is the story of a Friday, and the wee hours of a Saturday. It's a teacher training day, and Pipsqueak and his friends have no school.

In twenty-four hours, a sinister plot to take down a local business is launched, Snips and Snails dabble in the dark magic of Peyuase, a great deal of debauchery occurs, a cocktail of unrivaled destructive power is created and a small fleet of ships are launched! All of this and more, in Pipsqueak's Day Off!

Massive thanks to LittleSallyDigby for help, editing and advice.

Inexperience is a foreign concept to Celestia. At least she thinks it is. Right up until the moment a rash decision leaves her with a student who is a dozen years younger than what she's used to.

Enjoy.

This story is a sequel to Letters From a Friend at the End of the World

Her travels having brought her and her friends to the far-north city of Frostvale, Trixie finds herself caught up in a looming war and a dangerous plot. Still just trying to recover, she decides to lay low for a bit and wait for an opening to continue her journey.

Meanwhile, Twilight and friends continue following the trail Trixie left behind on her way north. By a combination of her letters, and the ponies they meet, they follow in her hoofsteps, discovering a number of surprising secrets along the way.

Thanks to both Belligerent Sock and Themaskedferret for pre-reading and editing.

Mort, also known as the Pale Pony (of Death), has been tasked to take time off from his rigorous duties of reaping souls. Seeking guidance, he is directed towards the town of Ponyville, to learn about the magic of friendship from Twilight Sparkle and her friends. All he needs to do is keep his true nature a secret. That shouldn't be too difficult...right?

Special thanks to Specter-Von-Baren and Pyrite Foolsgold for their help in proofreading and editing this story, as I really needed it. Additional thanks to Pilate, Chuckle5, Unimpressive Vagaries and Admiral Biscuit as well! Couldn't have done it without all their help!

Credit for the title card goes to Siansaar, AKA Carnifex.

For another excellent take on Mort, check out Sip's version!

For almost a year now, Trixie has been sending letters to Twilight. The only problem is, Twilight hasn't gotten a single one... until today. But now that she has, Twilight is left with more questions than she knows how to answer. Fortunately, she has a plan. Unfortunately, she doesn't know if that plan will work.

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Reading by: WhoLandon
Reading by: PonyFicsOutLoud

Twilight has been having her study sessions with the Cutie Mark Crusaders for some time, and has been remarkably pleased with their progress. And kind of worried, as they keep getting better and better. She might be a princess now, but TEACHING THE CUTIE MARK CRUSADERS? She'd rather not become their formal mentor. Yet.

A letter is sent out, and Princess Celestia gets a call for help. And, an opportunity is born. After all, why not? After a thousand years, perhaps it is time to do something else, just for a bit. She does have a rather wonderful younger sister who hasn't been ruling a land for a thousand years, and who has been studying how to rule for the past four rather intensely. So, teaching three fillies undercover? Sounds like fun.

And Luna. She's wanted to be as respected as her sister so much that she once went mad over it. But now, she's simply being handed the power that she once coveted for so long and no longer wants. What kind of a world does she live in now that her highest desire has been so casually granted?

With all of this, What Could Possibly Go Wrong?

Arcs:

Escape: When Celestia hears the call, she jumps at the chance to teach again, especially three fillies who might surpass her grandest student. But first she's got to escape her own identity...
Examination: So you want to find out what a filly does? Time to test her silly, so long as you don't taunt the Happy-Fun Filly.
Excitement: So, you've found the Happy-Fun Filly. Great, but the other two need help as well, and Scootaloo has this ~Great!~ idea for how to use her new-found magic...
Encouragement: Cometh the Bubbles, and a whole load of new headaches as they find out just what being a Happy-Fun Filly really means...
Exaltation: Where's Luna been this whole time? She can't be very happy about being left in the lurch holding Equestria. She could really use somepony to talk to.
Exercise: 'Sunbeam' is looking to teach the Happy-Fun Filly more, but first she needs to start taking care of the wagon-tire she keeps around her middle so that certain Unfun-Time Fillies don't interrupt her. And there's this big draft stallion looking for help...

Celestia and Luna have jointly ruled Equestria for centuries, and the land has been stable and prosperous under their rule, yet both of them have been slowly growing less and less enthused as the demands of their subjects begin to mount. As the two princesses approach their breaking points, it seems that the only thing that will stave off the destruction of Equestria is that both goddesses seem more focused on each other than the world at large. In the midst of this crisis, Twilight Sparkle, a newly commissioned officer in the Royal Guard, seeks what may be the only viable solution to this problem: locating the Elements of Harmony before either goddess can destroy them.

When the gym class teacher breaks her leg during a martial arts session, Principal Celestia and Vice-Principal Luna have to turn to someone they didn't want to turn to from the beginning.

Gunnery Sergeant Hartman.

Rated 'TEEN!(?)'
Expect swearing. Lots and LOTS of swearing, and also sexual humour.
Set within the Equestria Girls universe. Set before events of Sunset Shimmer's downfall.