Something has happened and Twilight finds herself in a strange and dark new world. The Bipeds here have strange magic, advanced technology, and a lot of problems. She needs a few friends, and they just might need her. WORM crossover. Deadpan29 has created some great supplementary material that is canon to the story.

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.

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injuries, almost incapable of using magic and haunted by the memories of her time on Earth, she becomes increasingly withdrawn from those who were closest to her.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!)

Applebloom just wanted to spend a day with her friends, crusading for her cutie mark. Instead, she found something even deeper and more troubling about herself. Turns out she's not even a member of the Apple Family by blood. In fact, she's not even truly native to Equestria! She's an alien! An alien robot no less!

Now Applebloom will have to deal with the reality of her origins and try to cope with them and her newfound abilities as she moves towards her future; a future that just might never come to be if her new foes have anything to say about it. Decepticons are, after all, a monstrous cabal.

Now, it's up to Applebloom to light Equestria's darkest hour.

Cover image credit goes to Inspectornills

Twilight Sparkle has too much magic, and it will take her decades to learn to control it. Her spectacular loss of control during her entrance exam only proves that fact. She is a danger to herself and others.

After Sunset Shimmer’s disappearance, Princess Celestia needs a new student to bear The Element of Magic to defeat Nightmare Moon. With all of Equestria at stake, Twilight Sparkle…is not the pony she needs.

Princess Celestia seals Twilight Sparkle’s magic with the distant promise of one day teaching her.

But there are two diarchs of Equestria. Amidst a lucid dream, an offer is made.

“Hello, Twilight. Would you like to be my student?”

Cover art provided by Lafiir.

Fashion shifts fast-forward for Rarity one fateful summer day. It's the day that her four future selves, each carrying a magical time amulet, show up in her studio! But will her destiny, her sister Sweetie Belle’s destiny – and the future for all Equestria for that matter - be irrevocably changed by what they tell her?

Update: Wow, put in 'Featured', 'Twilight's Library', and 'Celestia's Library'! I am honored.
Update to the Update: I'm on Equestria Daily? I am honored and flattered!!
Update to the Update to the Update: Youtube Video review by Strebiskunk!
Update to the Update to the...oh, you know the drill by now: 'Time Enough' has just been added to the elite 'Royal Guard' group of stories, huzzah!

While camping out in the mountains, Luna and Twilight enjoy a night relaxing under the stars, studying physics, and throwing rocks about.

Because every pony princess should learn how to raise a moon of her own.

Shortly after the defeat of Tirek, Princess Celestia began conducting a series of controlled and discreet experiments with a diverse family of potion types, one that allowed their alicorn users to safely witness and analyze events of the past. On the eve of the last of these such trials, a particularly potent potion among the others transports the Princess to a mysterious event far earlier in time than she had originally intended. 50,000 years earlier, in fact.

Now she's in the presence of a group of funny-looking hornless minotaurs wearing business suits.

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!)