Bioshock meets MLP in this psychological thriller, where Celestia's new faithful student, Siren Song, must discover the truth behind the city beneath the waves.

Beautiful, gifted, and faithful student of the Princess of the Sun, Siren Song has very nearly everything a pony could want. Sometimes though, in the twilight hours, Siren can see the sadness in her mentor's eyes. Once, ponies whisper, the Princess had another student named Twilight Sparkle, but she left Equestria, never to return. The pony who has a perfect life just needs one more thing—to convince Twilight Sparkle to come home so the Princess will smile again. But when Siren arrives in pursuit of Twilight, she soon finds herself trapped in a city of horrors, with only its monstrous denizens for help.

Now with a TV Tropes page!

Daniel Miller is one of the highest ranking members of the Fraternal Order of the Raven. Usually living a life of callous animosity, the Zealot soon finds himself pursuing his missing brother in an alien world filled with strange creatures and unlikely allies. However, Thomas' fate isn't the only reason for the Crow's arrival, and his ulterior motives may lead to dire consequences.

Sequel to "Where's the Fire?" which can be found here.

Bioshock: Infinite/MLP Crossover.

Thomas Miller proudly wore the armor of the feared Firemen of Columbia. Battle hardened and devoutly loyal; nothing could prevent one of Comstock's most elite soldiers from completing his mission. Even if that mission was to apprehend the Prophet's daughter, Elizabeth. He had a goal that no force on heaven or earth could stop him from achieving.....except perhaps Elizabeth herself.....

What happens when a pyromaniac finds himself dropped in the middle of Equestria?

Bioshock: Infinite/MLP crossover.

When Ruby boards the first trans-oceanic flight in Equestrian history, the last place she expects to end up is stranded in the middle of Eternity's Crossing in the wake of a horrific zeppelin crash. After a mysterious tower leads her and a fellow survivor to discover a twisted and fragmented city twenty thousand feet below the surface of the ocean, though, a bit of fire and smoke is the last thing she needs to worry about. Between the horrendously disfigured residents and the paranoia of the madmare who once built and controlled it, daily survival in this corrupted utopia is anything but a guarantee. But with the help of some new friends and a few genetic enhancements, Ruby isn't going down without a fight, and in the process might just discover that the deadliest weapon in Harmony is herself.

An adaptation of BioShock for the world of MLP. Written to be comprehensible to anyone, regardless of whether they've played the original game.

After a pickup mission gone wrong, a Huragok (Called Engineers by humans) crashes in the Everfree Forest. Witnessing the crash-landing and her curiosity getting the better of her, Apple Bloom finds the little gasbag. After a traumatic first encounter, she takes the biological supercomputer home. While she and the other ponies try to figure out what a Huragok actually is, they are completely unaware of the danger it poses to them.

Note: This story takes place sometime after the Halo novel The Thursday War by Karen Traviss

Dadab, the smartest Grunt in the Covenant, has mysteriously found himself in Equestria, and he's not alone. With him came an overly bossy Kig-Yar pirate, and a technophile Huragok. What shall the strange trio find in this magical new world? Glory? Fortune? Power? Or will they instead find more than they bargained for?

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 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!)

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!)

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!)