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

The Medallion of Light and the Medallion of Shadow are some of the most powerful yet obscure artifacts of antiquity. Created by a now-vanished cult of assassins, the two devices together give their bearer the incredible power to walk the worlds with but a single step.

Nefarious forces are closing in on both artifacts, and very little stands in their way. Heinrich Himmler's agents covet the medallions for the greater glory of the Third Reich. Ahuizotl's simply want their master to get what's coming to him: the world, and everything in it.

With the fate of all good people and ponies in doubt, one thing's for certain: saving two worlds would be one hell of an adventure. And if adventure has a name, it must be Daring Do… or is that Indiana Jones?

Will our heroes win the day? Find out in... Daring Do and the Medallion of Shadow! Or, Indiana Jones and the Medallion of Light!

NOTE: there will be some violence in this story, but nothing more than you would expect to see in an Indiana Jones movie-- so I didn't check the "gore" content box.

Artwork by Tzelly-el.

Special thanks to SapphireStarlightPony & Rated Ponystar for helping with the brainstorming on this one.

Thanks to this stupid thing I've had the Indiana Jones theme song stuck in my head for like the past four days and I am about to claw my eyes out AAAAAAAHHHHH @_@

Daring Do goes on an epic quest to cross magnificent landscapes, to scale impenetrable boundaries, and to transcend herself.

Epic Cover art by Dream0rDie

This story is a sequel to The Sisters Doo

Twilight Sparkle is a scientific pony. She understands things when they are explained.

Pinkie Pie is... uh... not a scientific pony. And she can't explain anything.

But there are secrets in the Wabe that Twilight needs to know, and only Pinkie has the answers.

A side-story to "The Sisters Doo".

Princess Twilight has brought Tirek to his knees with the aid of the alicorn magic given to her. Only this time, the wisdom of thousands of years allows her to see the only way to keep Equestria safe. With her nearly unlimited power, Twilight aims to ensure that evil never rises to threaten her kingdom again. The only way to do that is to stamp out the enemies of her kind one by one.

Contains Season Finale Spoilers.

Daring Do seeks a favor from her sister in Ponyville. Due to buried grudges, things quickly get out of hoof. She soon finds herself on her most perilous mission yet... with her biggest fan in the world. In the midst of truth and lies, loyalty and treachery, love and hate, one thing is clear ― some family situations are stranger than fiction.

The story extends in Through the Looking-glass and What Pinkie Found There and The Daughter Doo: Honorary Cutie Mark Crusader.

Many thanks to Honey Mead and statoose for their watchful and helpful pre-reading.

Ckat_Myla and statoose (CatNStat) have started an excellent reading of TSD.

An MLP/Warhammer 40K Crossover

The Iron Warriors 38th Company has landed in Equestria, entrenching themselves like a barbed hook. They hunt the aliens of the Tau Empire, intent on destruction and pillage.
A small squad is dispatched on a reconnaissance mission, only to find that there is intelligent life on this world besides the feuding space-farers.
Will these improbably adorable and friendly equine aliens turn the damned warriors of Chaos from their blood-soaked path, cleansing them of their dark legacy with the magic of friendship and harmony?

No.
No, that isn't happening.
EXPLOSIONS!!

(Dark humor warning; limited grimdark themes)
(Cover art by Nicholas Kay)
(This series now has its own TVtropes page!)
(This story is a contestant in the Tournament of Canterlot, a charity event to raise money for Syrian refugees! Go here for details and donations!)
(Featured on Equestria Daily 8/20/15 )

This story is a sequel to Iron Hearts: Book 3 - The Sept Lamman

An MLP/Warhammer 40K crossover, part 4.

The Tau threat has passed. The fleet that once thought to sweep aside the tainted pirates of the 38th Company has fled the system. The Lamman Sept is broken, demoralized, leaderless...
... And victorious.

With Lamman's plan put into motion, an alien horde hurtles through the Warp toward the Centaur system, its soldiers without number and thirsting for violence. Equestria's heroes must find a way to stop them, or the entire planet will be overrun with ease and its inhabitants butchered. While they could afford some pretense of neutrality and disinterest in the fight between the Iron Warriors and the Tau, now it is their world that lay in the crosshairs of the foe. Ponykind will need help to survive, and they look to the forces of Chaos for aid. But is there any hope to be found in the darkness?

EXPLOSIONS ARE IMMINENT.

(Dark humor warning; mild grimdark)
(Cover Art by Ahrimatt)
(This series now has its own TVtropes page!)
(This series is a contestant in the Tournament of Canterlot, a charity event to raise money for Syrian refugees! Go here for details and donations!)

This story is a sequel to Iron Hearts: Book 2 - Ferrous Dominus

An MLP/Warhammer 40K crossover, part 3.

The formal negotiations between Equestria and the Iron Warriors have failed. Yet peace and even cooperation between the harmonious ponies and the corrupted militants blooms in the dark corners of Canterlot and the open streets of Ferrous Dominus. The Elements of Harmony are safe, trade flourishes, and cautious meetings grow into lasting friendships as an unsteady calm descends upon both forces.
Even the Tau threat seems to have mysteriously vanished as the Iron Warriors refuse to assault their hideouts and risk springing the traps of the Fire Caste.
But the Tau have not vanished. The Lamman Sept of the Tau Empire, the Fire Caste's hidden dagger, have come to grips with the slumbering giant looming over their doorstep and have moved forward into the final phases of their plan. Fleets ply the void, hunters stalk the orchards, and in the depths of the badlands a strange device is rapidly assembled for purposes unknown.
The Tau alone know that time is running out, and more than just the fate of Centaur III hangs in the balance.

SIGNIFICANT POSSIBILITY OF EXPLOSIONS.

(Dark humor warning; minor grimdark)
(Cover art by Ahrimatt)
(This series now has its own TVtropes page!)
(This series is a contestant in the Tournament of Canterlot, a charity event to raise money for Syrian refugees! Go here for details and donations!)

What if, instead of going to Ponyville, Twilight Sparkle left Canterlot to go to the Pony Mesa Research Facility?
What if, instead of fighting off Nightmare Moon, she fought off a Resonance Cascade?
And what if, instead of meeting her friends in preparation for the Summer Sun Celebration, she instead met them in the aftermath of the Resonance Cascade?

This is the story of Twilight Sparkle, as she takes on the role of Gordon Freeman from the original Half-Life, and the friends she meets along the way.

Thanks to HiveLordLusa for the picture.