Nopony has heard from Fluttershy for three months. Not Rainbow Dash, not Rarity, not even Pinkie Pie. Her friends have been tending to the cottage and her animals, keeping it clean and organized, but even with Twilight's constant magic scans and a semi-constant guard search Equestria-wide, no hint has been found of where she went, how she vanished, or why she didn't tell anyone. Some ponies even think, in their darkest nightmares, that she might be dead.

Then she shows up one day, very definitely not dead, but just as definitely not the same as she was.

And does she have a story to tell. Boy, does she ever...

Coverart by Paladin.

After Planet Aether has been brought to peace and stabilized, Samus Aran doesn't get much rest when she's sent to reconnoiter a nameless planet on the edge of Galactic Federation space. Ostensibly, she was supposed to determine the size of a Space Pirate operation that was mining Phazon on this planet... and mark the place for a quick strike by Federation forces if it came down to it.

But when things become much more complicated beyond what her mission brief had stated, she may find that her fate and those of some unlikely allies may be intertwined. The battle that rages on the ground in a fight for survival and duty may have Samus questioning herself when a new front in an undeclared, nameless war is opened... in her mind.

-This is in no way related to Metroid Equis. No required reading, no relation, nothing. Pretend it does not exist.
-Takes place between Metroid Prime 2 and Metroid Prime 3. Metroid Timeline can be found here.
-Art by Pridark, sourced to her DA. Full picture is there.
-Story assumes very basic knowledge of Metroid universe, but I'll be doing my damndest to make this as accessible as possible.

Research log #579

It's been over one and a half years ago since the last activation of the device, though the magical signature hasn't changed it seems... weakened, to such a degree that the re-activation is impossible.

As described in the notes of research log #249 any attempt at providing the device an artificial source of magic to power failed, the device simply needed more energy than even the combined magical power of both Princess Luna and Celestia were capable of providing. You must be wondering now, I've already described these circumstances in previous logs so why bring it up now?

Simply said I'm out of options, every attempt of reactivating the device have failed and I'm only left with a single choice. I'm going to have to reverse engineer the device in an attempt to understand the mechanics with which it operates...

...At the risk of maybe never being unable to reconstruct it later.

I'm so sorry Fluttershy, I never should have involved you or any of the girls in the exploration of this structure. I hope that if we ever see you again you can find it in yourself to forgive me.

-Twilight Sparkle

In the true sense of Mass Effect, this story will be CYOA (Choose Your Own Adventure) giving you the reader the choice to decide the action of our protagonist.

I hope you enjoy!

Every chapter past chapter 27 was edited by gerandakis

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.

As fate would have it, Twilight had to hatch a much bigger egg this time.

Commander Shepard remembers firing the crucible. She remembers she had to make an important choice. She remembers good friends, a lover, and plenty of loyal crewmen.

She just can't remember what her choice was. What the threat she was striving so hard to end was. Or what the faces of the most important people in her life look like.

She also has no idea how she wound up in the monster filled forest she's come to call home for the past eight months. Or how she picked up a snarky A.I. making its home in her omni-tool.