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.

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.