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

Tiberium. The infamous green crystal that destroys entire worlds in its wake of global proliferation. It has been a little over a century since the Tiberium threat was first wiped out on Earth, and with it, the primary vestiges of the Brotherhood of Nod. When the GDI advanced humanity to the stars, they found that Earth had not been the only target of the alien Scrin: dozens of other worlds had already been claimed by Tiberium, and the Scrin returned in full force, attacking human colonies across space, stopping human expansion. To fight back, the GDI undergoes a reformation to become the Interstellar Defense Intiative (ISDI) and enacts the Hallman Directive, designed to stop Tiberium spread wherever it may be; such a protocol brings the reincarnated ITC Methuselah to a planet being ravaged by the green crystal, and the forces under Commander Martin Alexandra deploy to stop the threat.

Crossover Material: Command and Conquer - Tiberian Series/MLP
Rated Teen for Graphic Violence and Language

Humanity has grown to control most of the Sol system, and looks to distant stars for further expansion options. When probes discover an uncannily-earthlike planet at a vast distance, the Solar Government takes on a project larger than any before it.

A colony ship, carrying over seven thousand people, the Eclipse is constructed. Thanks to its translight engine, it is capable of making the journey within two decades. The expedition is launched with high hopes, its crew made up of the best and brightest, setting out to prove that the vastness of space was no longer an insurmountable obstacle, that landing on distant worlds full of life was no longer just a pipe dream.

What happens when this colony ship's crew arrives at their destination would forever change humanity's outlook on the rest of the universe, as well as what could be deemed possible. Supernatural beings, energies unexplainable, and most importantly, sapient organisms all populate this mysterious, fertile world. In all of its extensive preparations, is the Eclipse versatile enough to tackle the task assigned to it? Or, more importantly, is its crew?

Featured on Equestria Daily 1/1/2013.

Pre-read by Stringtheory and Milo. Proofread by Erumpet and Demetrius. Thanks! Contains some hard and some soft sci-fi elements.

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 Stardust

When Equestria’s newest member of royalty asks for aid to be offered to her friends from abroad, the best and the brightest volunteer to serve. Captain Steel Song of the Dusk Guard are immediately mobilized to help XCOM defend their world from the enemies that besiege them. However, their first joint operation with the humans takes a turn for the worse and they quickly find themselves fighting for their lives against the full force of the monsters that threaten Earth.

(Stardust/Dusk Guard crossover)
(Coverart provided by a friend of Viking ZX!)
(While familiarity with both stories isn’t required, it is recommended)
(Many thanks to Arzoo for pre-reading!)
(All screenshots can be found at XCOM.wikia.com)
(Featured on 3/13/2013. Thanks everyone!)
(Now has it's own section on TVTropes as part of the Stardust series!)

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!)

The star system Omega Centauri was just another oddity on a map to scientists in the not too distant future. However when they found the star was orbiting an earth-sized, earth-like planet instead of a black hole as its motion had suggested, a mission was scrambled to investigate this most unusual of celestial behaviors.

Hamstrung by politics, and nearly crippled before it began, the 'Lone Ranger' mission was reduced to just one crew member and left to his own devices.

These are the logs of Arrow 18 and its lone commander. This information is classified TOP SECRET by the Global Space Agency.

Do NOT tell the princess.

This story is a sequel to Awakening

This is the long dark night of the soul. More than 10,000 years have passed since Celestia’s reign over Equestria ended and the entire continent sank into the ocean and faded into myth and legend. Although the pony tribes have colonized the stars, the earth ponies have lost their connection to the land, the unicorns no longer think magic even exists, and the pegasus tribe has forgotten how to fly.
Although the principles of magic and friendship and Harmony are under constant assault in this age of war and strife, a pegasus named Thunder Gale has travelled to the ends of the galaxy in search of a long, lost friend of his. His search has led him to a planet where the old ways have not been entirely forgotten and evils left dormant since Celestia’s time stir once again. In order to survive the night, he’ll have to seek out guidance in the last place he ever thought of looking: the wings on his back.
Not a crossover nor an alternate universe, this is the far future and all this has happened before, and will happen again.
Cover art by Silfoe.
Now featured on Equestria Daily!