At the height of the EndWar, a Ghost team has orders to track down a madman who has kidnapped some of the United States' top scientists. However, when it turns out that the madman has used them to build a portal to escape from the world's ongoing onslaught, he runs through, forcing the Ghost team to follow through and take him down. In the aftermath of events, the Ghosts realize that they have no way to return home, and find themselves in a middle of a conflict that calls upon their talents to protect Equestria.

Crossover Material: Ghost Recon/MLP
Rated Teen for Graphic Violence and Language

Earth events take place in an alternate reality EndWar/Ghost Recon: Future Soldier.
Future Soldier technology is only drawn from initial previews of the game (exoskeletons, crosscoms, MR8s, rocket pods, active camouflage).

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

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.

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!)

A Metroid Crossover

A meteor, resistant to magical manipulation, crashes in Equestria, Planet Equis, and soon spreads an unknown poison throughout the land. Containment is all but failing and the Princesses have little power to stop the spread of the Great Poison. The Elements of Harmony are of little use as no knowledge exists of this threat that consumes all life. Help comes from a certain Hunter, clad in metal.

Samus Aran will not only fight for her life as always, but her own sanity as well as these ponies that she begrudgingly starts seeing as allies. New horrors and abilities await her as a reason to fight slowly festers within her, possibly unlocking something she had been denied for so long: Friendship.

Notes and Resources:

This takes place after Echoes. The events of Corruption will have not happened yet. In terms of MLP, consider everything up to and including the Crystal Empire. Princess Twilight does not exist here, etc. The official Metroid Timeline can be found here.

As well, this story references the manga in many places. Reading of it is not required and I try my best to explain the context, but if you're interested, both volumes can be found here.

EDIT: This story was written over two and a half years, beginning in 2013. You'll probably notice the difference in writing as the chapters progress.

It took many long years and far more defeats than he'd care to admit, but at last—at long last—victory was finally within the great Ahuizotl's reach. Absolutely nothing, not even that meddlesome Daring Do, would be able to stand in his way any longer. Yet even with his arch nemesis facing her inevitable demise and the ultimate power literally in his grasp, he can't shake the feeling that he's forgotten about something.

One tiny, crucial detail. Something very important. As in, 'could easily ruin his plans if not attended to' important.

...

Eh, maybe he just left the oven on again.

A long time ago, in a galaxy far, far away...

Shortly after the Second Battle of Geonosis, a Republic probe reports the discovery of a new planet outside of their galaxy, a seemingly insignificant occurance, if not for the CIS frigate seen orbiting the planet. Curious to see what the Separatists have found, the Republic sends a cruiser to the planet, only to be suddenly ambushed by several CIS ships. Determining that the CIS has discovered something important and prehaps vital to their war efforts, Mace Windu and Obi-Wan Kenobi dispatch Victor Squad, a group of...special clones, to the planet's surface to investigate it.

Their mission carries more weight than they think.

Shoutouts to Nathan, my friend Fernando, kento124, and to Legion222 for proof reading and editing.
Shoutout to Ultima Fatalis on DeviatArt for the awesome cover art.

Follows MLP canon excluding S3E13 and beyond as closely as possible.

If you're going to dislike, at least have the courtesy to explain why.

Undeservedly featured on 6/15/2015. Not sure why, but hey, that's cool.

A close encounter with a category three Kaiju leaves Midsummer Night, a Mark-II Jaeger, in the inky depths of an unknown ocean. With no communications or navigation available, the pilots, Shane and Michael O'Connell, are well and truly out of their element.

Good thing they accidentally brought something with them to liven up the party,

Pacific Rim crossover

Art by: Zeiram0034.
Edited by: Pixel brony.

Now with a Tvtropes page!

Death. All that remains on this planet are the martyrs who gave their lives to ensure the others could escape. Humanity’s greatest has fallen. 23 Billion humans died in the war, and only more would follow. The few strays on Reach were quickly found and slaughtered. The last soldier died fighting, a fitting tribute to the planet humanity fought so hard to protect. Still, the story is not over for mankind, just as the story is not over for this lone soldier. This, is the story of Noble Six.

Coverart by CCNC, link to her deviantart http://ccncc.deviantart.com/

Edited by Escaping Reality