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

This story is a sequel to Project: Sunflower

No story ever truly ends, and some stories have parts that remain hidden until they are unearthed.

This will be a collection of stories related to Project: Sunflower. Stories as yet unheard, and things that come after the end.

Note:
The stories presented here will be slice-of-life style stories based in the same universe as Project: Sunflower, and therefore will contain spoilers. It is recommended that you read Project: Sunflower before reading these stories.

These will not necessarily be in chronological order, and each side story will contain a note describing when it takes place in the main story time line.

(Additional characters/tags may be added as the stories require)

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!)

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 Twilight Goes to Dalaran

A tauren, an undead and an alicorn go into a tavern.

A short story about orcs, drinks and axes. Do not attempt this at home.
You don't need to know the game to follow the story but having read the prequel is strongly recommended.

'I looked at the reflection, and the beast looked back.'

Viktoria had never seen the mirror before, now she wishes she had never examined it. With her body twisted into a strange and unsettling new shape she must become accustomed to her new equine form before finding a way home, and along the way also return her body to normal. Her body betrays her with each movement, muscle memory working against her. Will the newly encountered Flitter and Cloudchaser be able to help her?

Even with the new addition of wings to grant her flight and escape, Viktoria has never felt more confined.

'Others see me for what I am. I only wish for them to see me for who I am.'

( Thanks go to AkuOreo for such a lovely cover art! )

( Also, seems to have a Tv tropes page in the making! )

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.

After a portal experiment goes terribly wrong, Twilight finds herself on a strange world full of bipedal, magical creatures. She has no idea how to get back home. Maybe her new friends, a young Tauren and an Undead, can help her. They know of a magical city in the sky which might hold the answer to her problem. But can she really trust anybody in a world where true friendship is a rarity?

Knowledge of the Warcraft universe is not necessary to understand this story - but it might make reading it more fun.

The Mane Six, Spike, and the two alicorn princesses are sucked into an alien world. They soon discover that they have been transported to a galaxy far, far from home. A galaxy which is under the control of the evil Galactic Empire and where Emperor Palpatine knows of them and wants to use them for his own nefarious purposes.

Twilight must lead her friends on their journey through a cruel and hostile galaxy, avoiding the Imperial forces and bounty hunters sent after them, trying to find the Rebel Alliance.

They may be the ponies' only hope for getting home . . . .

Bonus: here's the main title music for this story https://www.youtube.com/watch?v=QB4xZpWumYg

Friendship, the Final Frontier.
When a Starfleet ship discovers that the Orion Syndicate is enslaving ponies, her commander decides to do a good deed and return the rainbow-maned pegasus home to Equestria. Things don't go smoothly for the crew of the USS Judges, but what they find may be one of their biggest discoveries ever.
A Friendship Is Magic/Star Trek Online crossover.