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!)

For some, it all started as a relaxing day at the spa. For another, it started with a space bridge malfunction. When a mysterious creature crash lands into the woods on the outskirts of Ponyville, Twilight Sparkle and the bearers of the Elements of Harmony must investigate the circumstances that brought this life form to Equestria, and face an unyielding force of evil that threatens their entire world. (warning: Mild language, violence)

After her humiliating defeat at the hooves of Princess Cadence and Shining Armor, Queen Chrysalis and a small cadre of her Changeling minions find themselves lost on a lonely mountain deep in the Everfree Forest. With a storm brewing, she decides to take shelter in a cave along the Mountainside.

Unfortunately, the cave is already occupied. Queen Chrysalis and her forces are swiftly surrounded by the Predacons. However, before hostilities commence, Megatron makes her an offer. An offer she would be an idiot to refuse.

Sequel to "My Little Pony: Flesh and Steel", which can be found here

This is an idea that wouldn't leave my head, inspired by Fairy Slayer's "Mommy Nearest," Aldea Donder's "Alicorn," SoundofRainfall's "Play" and RainbowDoubleDash's "Lunaverse"

Alternate Universe: Instead of Twilight Sparkle, Princess Celestia made Rainbow Dash her personal student instead! Follow her through the events of the 1,000th Summer Sun Celebration. A reimagining of "Friendship is Magic"

An object of unknown origins crash lands in the no-pony's land between Equestria and Gryphon territory. Princess Luna and Twilight Sparkle race to beat the Gryphons to the crash site, but discover more to the crash than they originally thought.

Princess Twilight Sparkle is perfectly happy with her perfectly ordinary life in Ponyville. Every library book is properly shelved in its appropriate place, and her life continues on exactly according to her meticulously planned out schedule.

Then she gets a bodyguard.

Now she has to find some way to fit this new pony into her life on short notice. It won’t be an easy thing to adjust to—especially since Captain Storm Kicker’s presence makes it that much harder for her to go on living like the same old Twilight Sparkle she was before she became a princess.

Reader, in ancient days, the old lords of the world numbered in thousands. Then hundreds. Then even less.
Now, they are found only in tapestries and fanciful ballads.
The creatures are all vanished. All but one.

Rumors say there are more of him, somewhere far away. A young and supposedly gifted mage called Star Swirl, and Heartstrings, a gentle spinster, have joined him on a journey to find the rest.

Featured in The Royal Guard's Fic Spotlight #5
TV Tropes page (that could use more love)

Night and day. Fire and ice. Creation and destruction. Everything has an opposite, and Chaos is no exception. Princess Celestia tells Twilight the true history of Discord's rise, the Alicorns' fall, and the creation of the Elements of Harmony.

She tells her student the story of Order and Chaos.

Once, I was alone.

I felt neither sorrow nor joy at this. The presence or absence of others meant nothing to me. The universe moved in silence, and I drifted in its flow.

Then came the song.

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page