This story is a sequel to Foal of the Forest

Second story of the Savage Skies series:
Dawn Lightwing has overcome many trials in his life; persecution for his unique eyes, living amongst the monsters of the Everfree Forest. But now all of that is behind him. He's been adopted by Fluttershy, mended from his conflict with Applejack, and now sits poised to go to school and live the life of a normal foal. Unfortunately, Dawn's past is not so far behind him as he would like, as his experiences have left scars on his mind and heart that threaten everything he has gained since coming to Ponyville.

Followed by Storm on the Horizon.
Now with a TV Tropes page.

This story is a sequel to The Promise of a New Day

Story three of Savage Skies:
All sorts of things are brewing in the pegasus city of Cloudsdale, which is a problem for Ponyville as the one thing that isn't is a rainstorm. As the drought continues to drag on, Rainbow Dash must confront her hometown and its history, as well as her own history. But she won't do it alone, which is good, because she'll need all the help she can get.

Series starts with Foal of the Forest.
Now with a TV Tropes page.

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.

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!)

Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?

"In short, it's a story of friendship and plasma rifles, with the emphasis on the friendship. The characters are well written, the XCOM setting is fleshed out very well, and the story is compelling. If you love XCOM, you'll love the story, but even if you've never heard of it, it's more than worth giving the first 3 chapters a read.

There's excellent action later on, but the real strength lies in the collision between the friendly and naive world of Twilight Sparkle and the desperate world of humans fighting a losing war for survival and willing to do anything to turn the tide."

--Arzoo

(XCOM/FiM crossover)
(Cover art commissioned by a friend and created by the magnificent FoxInShadow!)
(Original cover art by the amazing Carnelian can be viewed here!)
(Gore tag for blood and some violence)
(Many thanks to the studius OminousTen, Arzoo, xXFluttershyForeverXx and finally Setokaiva for giving my rambles a once-over)
(Now with it's own TV Tropes page! Get to tropin' folks!)

Brought to you by Loyal2Luna, this new Downloadable Content for Mass Effect 2 brings the fight to Equestria.

Just about ready to embark on their mission to stop the Collectors from further abducting human colonies, Commander Shepard and the crew of the Normandy SR-2 are given a new priority, when the Illusive Man tasks them with investigating the mysterious disappearance of a Cerberus science team.

Soon, what begins as a simple search-and-rescue unveils a mystery millions of years in the making, and the Commander finds himself thrust into a situation he couldn't possibly have prepared himself for.

Join the Hero of the Citadel as he uncovers the secrets, combats the demons, and ultimately decides the fate of the impossible world known as "Equestria."

Scootaloo is a young pony who has endured quite a bit of hardships, but has made the best of her life, even if it hasn't always been so easy. The little filly from Port Mane shares, in her own words, the ups and downs of her life, and just what it means to endure.

Find out how Scootaloo has endured through love and loss. See her thoughts on Rainbow Dash, her family, the crusaders, Featherweight, Pipsqueak, Diamond Tiara, Silver Spoon, Princess Luna and more.

Thanks to user sqarishoctagon for helping me edit. Soundtrack added via YouTube.

[Image is deceptive, it's not always as sad as the image implies, there's all kinds of moods, but this is a pic I'm proud of, and it's relevant in parts. Also check this description for more pics as the story unfolds.]

THIS IS A SIMILAR BUT DIFFERENT UNIVERSE. I wrote this, starting during late Season 2, so I had to make judgment calls based on the information I had. As such, certain episodes thereafter do not match up, or fit in different places. Consequently, it is a very similar alternate universe. Many events happen in both this and the show timeline, but do not always match. I tried to stay consistent when possible, but certain things were lost to disagreements in interpretation. I like how I wrote my story and will not force it to match what came after I started writing. I've also decided to consider this fluidly finished. I still seem to make updates, but I no longer guarantee them.

[Please, if you read this, let me know what you think. PM me, comment, whatever. I just really want to hear people's thoughts!]

Pictures of the OCs:

Auntie Raincloud: http://fav.me/d57lxyk
Rosy Fields: http://fav.me/d57lxsb
Thunderclap: http://fav.me/d57lxv5
Miss Golden Posey: http://fav.me/d57m7on
Shooting Star: http://fav.me/d57mfah
Lucky Buck: http://fav.me/d57mf6t
Shutter Speed: http://fav.me/d57vow5
Ocean Breeze: http://fav.me/d57ly1b
Maple Woods: http://fav.me/d57m5dq
Sandy Shores: http://fav.me/d57m5gl
Cherry Tart: http://fav.me/d5mb5ch
Blazemane: http://fav.me/d57wlua
Thunderbolt: http://fav.me/d57wm42
Winter Winds: http://fav.me/d57wlwl
Wild Wisp: http://fav.me/d57wm2h
Jasmine Tea: http://fav.me/d6hb1kx
Golden Manchet: http://fav.me/d6hazp7 (Turned out greener than I intended.)

*THANKS TO EVERYONE who has given this a 95+% positive rating after over 3000 views 800 comments and 550 votes! I'm so thankful for your enjoyment of the story!*

Story events/characters that could spoil things:

http://fav.me/d8upn3c - My own art
http://fav.me/d8upn2w - My own art
http://fav.me/d8upf61 - My own art
http://fav.me/d8un0gx - My own art
http://fav.me/d8uqb91 - My own art
http://fav.me/d8urrbn - My own art
http://fav.me/d8uwzxl - My own art -- SPOILERS
http://fav.me/d6h2xa6 - Commissioned
http://fav.me/d6fvi4w - Commissioned
http://fav.me/d6fspin - Commissioned
http://fav.me/d6fp5eb - Commissioned
http://fav.me/d6h7t30 - The photograph from Entry 35. Faded as found.
http://fav.me/d6gcugr - Scootaloo's Family Portrait ca. Entry 43. Commissioned and lovely.
http://fav.me/d8y4c5t - Commissioned art portraying an event from the final two chapters. (Spoilers.)
http://fav.me/d53luw1 - Legitimate fanart. GREATLY appreciated.

http://fav.me/d8wy111 - a picture of Lucky Buck created from an art prompt "Starstruck"