The Princesses find an alien creature barely clinging to life at the scene of a terrifying crash. Can the Combined Power of the Elements of Harmony save it, or more importantly, should they save it? Will the arrival of this strange creature tear Equestria apart?

TV Tropes
https://tvtropes.org/pmwiki/pmwiki.php/FanFic/Article2

Equestria is still picking up the pieces after the defeat of Tirek, and everypony is helping out with the paperwork, even Rainbow Dash. Things change when Princess Celestia arrives, bringing with her a letter with some very stunning accusations of the exploits of a resident in the town of Oasis. Now, the main six are tasked with finding out if the letter was truth or fiction. Did this Mister Baker really do what they claim? Only one way to find out.

However, Mister Baker is not who, or what they expected.

Rated Teen for occasional language. Additional tags added for more dark themes.

Proof read and edited by the amazing SunnyPack , Snakeskin Ducktape, and Tyrannosaurus Tux.

This story is a sequel to What I've Become

It is highly recommended that you read What I've Become before you read this story, since this is the second story in The Humanity Within Trilogy, and you will be lost if you just plunge into this without any preparation.

Also, this story already has a sequel: What I Am!

Things have been turning up roses for me lately. I'm no longer fighting to survive, I have people that I can turn to, and I have my face back, all because of the kindness shown to me by strangers.
But will they continue to help me once they find out what dark secrets haunt my past? Will they shun me for the evil deeds that my abductors forced me to do while I was in their service? Will they continue to protect me from the monsters that destroyed my life, once they realize what kind of monster I really am?
How does one forgive a murderer?
WOOT! Feature the day it came out! (how did that happen?) 12/1/2014
Edited by Malefactory. He is fantastic at this kind of thing!
Proofread by Cantankerous. He's freaking amazing.
Also proofread by PhiliChez.
Cover Image done by the very talented PaintSplotch! You can find his FimFic account here.
And here is his DeviantArt Account!

It is the year 2038, and the Earth is slowly being consumed by a space-borne monstrosity dubbed the Black Tide, which is using nanotechnology to remake the planet into something hideously alien.

Erin Olsen works for Project Harmonics, humanity's last-ditch effort to find a new world before the Tide can wipe them out. But when that world is found, and it turns out to be occupied, Erin will need to find the courage to face the unknown in order to save the inhabitants of both worlds.

(Many thanks to Easteu for the fantastic cover image for this story!)

Now with its own TV Tropes page

There is now a follow-up to this story: Sunflower - Side Projects
Sequel: Project Sunflower: Harmony

Fluttershy is used to nursing critters of all sorts back to health. When she comes across a broken showmare, however, it will take all her patience and care to help the other pony. Especially when Trixie begrudges her help every step of the way. Can she get through to her? And can Trixie learn that she doesn't need to stand alone to stand strong?

Celestia had always thought she'd reached the pinnacle of fear when she fought against some of Equestria's greatest enemies.

As it turns out, however, nothing compares to explaining to Twilight's parents that she's in a relationship with their daughter.

This story is a sequel to Stardust

Times are changing for Equestria as Twilight’s return brings with it news of people and cultures from beyond the peaceful world everypony knows. Aid and volunteers are freely offered to help the besieged humans of Earth because every Equestrian knows that’s what good friends do. Unfortunately, making friends can also have the unintended consequence of making enemies.

When the monsters besieging the humans strike at Equestria with a level of brutality not seen in over a thousand years, the cry for help is sent to all the kingdoms of the world. Honored allies step forth to fulfill ancient treaties and oaths. Enemies, old and new, bury their grievances. An alliance never before seen in Equestria will be created to combat the monsters from the void.

And because of these events, a grim but welcome sibling to the XCOM project is born.

(XCOM/FiM Crossover)
(Sequel to Stardust, which I recommend reading before starting this. Fortitude Amicitia and Broken aren't required reading but are supplemental to the storyline)
(Gore tag for blood and violence)
(Alternate Universe tag because of the divergence from canon that Stardust has caused)
(Uses elements of Season 4)
(Coverart produced by the amazing Carnelian!)
(Many thanks to Arzoo, BradTheBrony, Vandenbz and Setokaiva for prereading!)
(As of 03/07/2016, the prereading team consists of Arzoo, BradTheBrony, Noble Cause and Metallusionsismagic!)
(Complete with it's own TVTropes page as part of the Stardust continuity. Could use some updating!)
(Character tags will be added as chapters are added!)
(Featured 5/12/2014! Thanks folks!)
(Possible spoilers in the comments! BEWARE!)

This story is a sequel to Stardust

Twilight has finally returned home from the harrowing challenge that Discord set upon her, and the residents of Ponyville and the Elements especially look forward to having their dear friend returned to them.

Twilight, however, has changed. Still suffering from her injuries, almost incapable of using magic and haunted by the memories of her time on Earth, she becomes increasingly withdrawn from those who were closest to her. Will her frustration at her current state and her friends inability to understand her experiences cost her what she valued most before Discord's bet?

(Sequel to Stardust, familiarity with this is recommended!)
(Proofread by Arzoo!)
(Coverart commission drawn by the amazing KairaAnix!)
(Crossover with XCOM: Enemy Within, though the crossover and human elements are minimal)
(Featured 4/28/2014, thanks folks!)

This story is a sequel to Project: Sunflower

After the events of Project: Sunflower, Erin Olsen has returned to Ponyville, happy to pursue her studies in magic. After everything that happened the year before, she's looking forward to spending her days studying and having fun with her friends.

Meanwhile, on the newly discovered world of Harmony, humans and ponies work together to study this strange new world. However, their arrival causes something ancient to begin stirring. Something that may end up changing everything.

Erin will need all of her courage, all of her cleverness and, of course, all of her friends to see herself through what happens next.

Cover art by Valkyrie-Girl
Editing provided by:
Brilliant Point, Coandco, Ekevoo, Ludicrous Lycan, Merlos the Mad and Razalon the Lizardman.

Fantastic, I finally get to visit my favorite cast of awesome talking ponies to have one small thing keeping me from enjoying it to its fullest. I CAN"T FREAKING INTERACT WITH ANYTHING. I guess being a ghost in Equestria isn't the worst thing that could have happened, at least I can shadow my favorite ponies and see what going on in their lives. Heh, I guess I've become the ultimate stalker, I do miss having someone to talk to that wasn't me, myself or I though.

*^*^*
Set before the events of season three.

Rated teen for now for safety, rating may change later on based on where the story goes. Characters will be added later if they get added to the story.